chr12-57626577-A-G

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001478.5(B4GALNT1):​c.*167T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 768,280 control chromosomes in the GnomAD database, including 15,427 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2646 hom., cov: 32)
Exomes 𝑓: 0.20 ( 12781 hom. )

Consequence

B4GALNT1
NM_001478.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.32
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 12-57626577-A-G is Benign according to our data. Variant chr12-57626577-A-G is described in ClinVar as [Benign]. Clinvar id is 1242221.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
B4GALNT1NM_001478.5 linkuse as main transcriptc.*167T>C 3_prime_UTR_variant 11/11 ENST00000341156.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
B4GALNT1ENST00000341156.9 linkuse as main transcriptc.*167T>C 3_prime_UTR_variant 11/111 NM_001478.5 P1Q00973-1

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27354
AN:
152000
Hom.:
2640
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.120
Gnomad AMI
AF:
0.158
Gnomad AMR
AF:
0.245
Gnomad ASJ
AF:
0.112
Gnomad EAS
AF:
0.132
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.200
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.209
Gnomad OTH
AF:
0.165
GnomAD4 exome
AF:
0.198
AC:
122128
AN:
616162
Hom.:
12781
Cov.:
8
AF XY:
0.194
AC XY:
62194
AN XY:
320070
show subpopulations
Gnomad4 AFR exome
AF:
0.121
Gnomad4 AMR exome
AF:
0.289
Gnomad4 ASJ exome
AF:
0.125
Gnomad4 EAS exome
AF:
0.111
Gnomad4 SAS exome
AF:
0.140
Gnomad4 FIN exome
AF:
0.207
Gnomad4 NFE exome
AF:
0.214
Gnomad4 OTH exome
AF:
0.186
GnomAD4 genome
AF:
0.180
AC:
27375
AN:
152118
Hom.:
2646
Cov.:
32
AF XY:
0.178
AC XY:
13235
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.120
Gnomad4 AMR
AF:
0.245
Gnomad4 ASJ
AF:
0.112
Gnomad4 EAS
AF:
0.132
Gnomad4 SAS
AF:
0.152
Gnomad4 FIN
AF:
0.200
Gnomad4 NFE
AF:
0.209
Gnomad4 OTH
AF:
0.167
Alfa
AF:
0.187
Hom.:
621
Bravo
AF:
0.182
Asia WGS
AF:
0.135
AC:
473
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.38
CADD
Benign
12
DANN
Benign
0.77

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs35831868; hg19: chr12-58020360; API