rs7131938

Variant names:

• chr12-53379143-C-T
• rs7131938
• ENST00000791529.1:n.*64G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000791529.1(ENSG00000303057):​n.*64G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,084 control chromosomes in the GnomAD database, including 4,116 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4116 hom., cov: 32)
• Consequence: ENSG00000303057 ENST00000791529.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 14 publications found

Genes affected

ENSG00000303057 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303057	ENST00000791529.1	n.*64G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34842 AN: 151966 Hom.: 4109 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.203

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.229 AC: 34871 AN: 152084 Hom.: 4116 Cov.: 32 AF XY: 0.231 AC XY: 17171 AN XY: 74316

African (AFR) AF: 0.221 AC: 9154 AN: 41496

American (AMR) AF: 0.240 AC: 3663 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3468

East Asian (EAS) AF: 0.201 AC: 1040 AN: 5166

South Asian (SAS) AF: 0.333 AC: 1603 AN: 4810

European-Finnish (FIN) AF: 0.229 AC: 2418 AN: 10582

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15507 AN: 67966

Other (OTH) AF: 0.209 AC: 441 AN: 2112

Alfa AF: 0.226 Hom.: 10556

Bravo AF: 0.224

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.6
DANN	Benign	0.85
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7131938; hg19: chr12-53772927;