chr12-57625419-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_001478.5(B4GALNT1):​c.*1325G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 1,614,136 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0024 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 13 hom. )

Consequence

B4GALNT1
NM_001478.5 3_prime_UTR

Scores

1
3
3

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.629
Variant links:
Genes affected
B4GALNT1 (HGNC:4117): (beta-1,4-N-acetyl-galactosaminyltransferase 1) GM2 and GD2 gangliosides are sialic acid-containing glycosphingolipids. GalNAc-T is the enzyme involved in the biosynthesis of G(M2) and G(D2) glycosphingolipids. GalNAc-T catalyzes the transfer of GalNAc into G(M3) and G(D3) by a beta-1,4 linkage, resulting in the synthesis of G(M2) and G(D2), respectively. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2013]
SLC26A10P (HGNC:14470): (solute carrier family 26 member 10, pseudogene) Predicted to enable anion transmembrane transporter activity. Predicted to be involved in anion transport. Predicted to be active in basolateral plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6
Variant 12-57625419-C-T is Benign according to our data. Variant chr12-57625419-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1686497.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=2}.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00239 (364/152260) while in subpopulation AMR AF= 0.00608 (93/15302). AF 95% confidence interval is 0.00508. There are 2 homozygotes in gnomad4. There are 171 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
B4GALNT1NM_001478.5 linkuse as main transcriptc.*1325G>A 3_prime_UTR_variant 11/11 ENST00000341156.9
SLC26A10PNR_166679.1 linkuse as main transcriptn.2272C>T non_coding_transcript_exon_variant 14/16

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
B4GALNT1ENST00000341156.9 linkuse as main transcriptc.*1325G>A 3_prime_UTR_variant 11/111 NM_001478.5 P1Q00973-1
ENST00000440686.5 linkuse as main transcriptn.1450C>T non_coding_transcript_exon_variant 14/162
SLC26A10PENST00000665594.1 linkuse as main transcriptn.1879C>T non_coding_transcript_exon_variant 16/18

Frequencies

GnomAD3 genomes
AF:
0.00239
AC:
364
AN:
152142
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000652
Gnomad AMI
AF:
0.00658
Gnomad AMR
AF:
0.00609
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00326
Gnomad OTH
AF:
0.00383
GnomAD3 exomes
AF:
0.00237
AC:
597
AN:
251456
Hom.:
5
AF XY:
0.00255
AC XY:
347
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.000615
Gnomad AMR exome
AF:
0.00573
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000686
Gnomad FIN exome
AF:
0.000139
Gnomad NFE exome
AF:
0.00309
Gnomad OTH exome
AF:
0.00228
GnomAD4 exome
AF:
0.00270
AC:
3941
AN:
1461876
Hom.:
13
Cov.:
38
AF XY:
0.00266
AC XY:
1935
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.000478
Gnomad4 AMR exome
AF:
0.00597
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000707
Gnomad4 FIN exome
AF:
0.000243
Gnomad4 NFE exome
AF:
0.00304
Gnomad4 OTH exome
AF:
0.00310
GnomAD4 genome
AF:
0.00239
AC:
364
AN:
152260
Hom.:
2
Cov.:
32
AF XY:
0.00230
AC XY:
171
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.000650
Gnomad4 AMR
AF:
0.00608
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.00326
Gnomad4 OTH
AF:
0.00379
Alfa
AF:
0.00187
Hom.:
1
Bravo
AF:
0.00261
TwinsUK
AF:
0.00270
AC:
10
ALSPAC
AF:
0.00337
AC:
13
ESP6500AA
AF:
0.000681
AC:
3
ESP6500EA
AF:
0.00326
AC:
28
ExAC
AF:
0.00227
AC:
275
EpiCase
AF:
0.00403
EpiControl
AF:
0.00451

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingMendelicsMay 04, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.042
T
BayesDel_noAF
Pathogenic
0.29
CADD
Benign
16
DANN
Uncertain
0.99
Eigen
Uncertain
0.27
Eigen_PC
Benign
0.0046
FATHMM_MKL
Benign
0.13
N
MutationTaster
Benign
1.0
D;N
Vest4
0.078
GERP RS
2.2

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs151077423; hg19: chr12-58019202; API