chr1-99993238-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The ENST00000533028.8(SLC35A3):​c.-18-299G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 221,402 control chromosomes in the GnomAD database, including 107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.025 ( 64 hom., cov: 32)
Exomes 𝑓: 0.032 ( 43 hom. )

Consequence

SLC35A3
ENST00000533028.8 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0260
Variant links:
Genes affected
SLC35A3 (HGNC:11023): (solute carrier family 35 member A3) This gene encodes a UDP-N-acetylglucosamine transporter found in the golgi apparatus membrane. In cattle, a missense mutation in this gene causes complex vertebral malformation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 1-99993238-G-A is Benign according to our data. Variant chr1-99993238-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1189507.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0248 (3781/152230) while in subpopulation NFE AF= 0.0397 (2702/68006). AF 95% confidence interval is 0.0385. There are 64 homozygotes in gnomad4. There are 1784 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 64 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC35A3NM_012243.3 linkuse as main transcriptc.-18-299G>A intron_variant ENST00000533028.8 NP_036375.1
LOC124904230XR_007066249.1 linkuse as main transcriptn.279+44492C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC35A3ENST00000533028.8 linkuse as main transcriptc.-18-299G>A intron_variant 1 NM_012243.3 ENSP00000433849 P1Q9Y2D2-1

Frequencies

GnomAD3 genomes
AF:
0.0249
AC:
3785
AN:
152112
Hom.:
64
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00705
Gnomad AMI
AF:
0.0439
Gnomad AMR
AF:
0.0149
Gnomad ASJ
AF:
0.0308
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00747
Gnomad FIN
AF:
0.0296
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0397
Gnomad OTH
AF:
0.0244
GnomAD4 exome
AF:
0.0318
AC:
2198
AN:
69172
Hom.:
43
AF XY:
0.0312
AC XY:
1144
AN XY:
36720
show subpopulations
Gnomad4 AFR exome
AF:
0.00614
Gnomad4 AMR exome
AF:
0.0213
Gnomad4 ASJ exome
AF:
0.0389
Gnomad4 EAS exome
AF:
0.000288
Gnomad4 SAS exome
AF:
0.00957
Gnomad4 FIN exome
AF:
0.0363
Gnomad4 NFE exome
AF:
0.0392
Gnomad4 OTH exome
AF:
0.0322
GnomAD4 genome
AF:
0.0248
AC:
3781
AN:
152230
Hom.:
64
Cov.:
32
AF XY:
0.0240
AC XY:
1784
AN XY:
74444
show subpopulations
Gnomad4 AFR
AF:
0.00700
Gnomad4 AMR
AF:
0.0148
Gnomad4 ASJ
AF:
0.0308
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00747
Gnomad4 FIN
AF:
0.0296
Gnomad4 NFE
AF:
0.0397
Gnomad4 OTH
AF:
0.0241
Alfa
AF:
0.0331
Hom.:
23
Bravo
AF:
0.0238
Asia WGS
AF:
0.00375
AC:
14
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxSep 04, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
4.1
DANN
Benign
0.51

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: rs72728114; hg19: chr1-100458794; API