rs3130977

Variant names:

• chr6-31114212-T-C
• rs3130977

Variant summary

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

The variant allele was found at a frequency of 0.298 in 151,924 control chromosomes in the GnomAD database, including 6,798 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 0.30 (6798 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) 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

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45218 AN: 151806 Hom.: 6786 Cov.: 30

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.298 AC: 45265 AN: 151924 Hom.: 6798 Cov.: 30 AF XY: 0.295 AC XY: 21919 AN XY: 74258

African (AFR) AF: 0.270 AC: 11177 AN: 41412

American (AMR) AF: 0.269 AC: 4117 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1075 AN: 5170

South Asian (SAS) AF: 0.306 AC: 1477 AN: 4826

European-Finnish (FIN) AF: 0.309 AC: 3260 AN: 10538

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21982 AN: 67920

Other (OTH) AF: 0.308 AC: 647 AN: 2102

Alfa AF: 0.319 Hom.: 32349

Bravo AF: 0.294

Asia WGS AF: 0.256 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	11
DANN	Benign	0.86
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs3130977; hg19: chr6-31081989;