rs3130473

Variant names:

• chr6-31231431-C-T
• rs3130473

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 0.227 in 152,004 control chromosomes in the GnomAD database, including 4,044 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 (4044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.38
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.14).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 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: 0.227 AC: 34508 AN: 151886 Hom.: 4043 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.227 AC: 34515 AN: 152004 Hom.: 4044 Cov.: 32 AF XY: 0.223 AC XY: 16560 AN XY: 74280

African (AFR) AF: 0.172 AC: 7140 AN: 41456

American (AMR) AF: 0.197 AC: 3015 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 999 AN: 3468

East Asian (EAS) AF: 0.289 AC: 1497 AN: 5180

South Asian (SAS) AF: 0.215 AC: 1037 AN: 4816

European-Finnish (FIN) AF: 0.180 AC: 1899 AN: 10538

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18016 AN: 67950

Other (OTH) AF: 0.240 AC: 507 AN: 2110

Alfa AF: 0.253 Hom.: 15440

Bravo AF: 0.225

Asia WGS AF: 0.220 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.42
DANN	Benign	0.77
PhyloP100		-5.4

Splicing

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

Other links and lift over

dbSNP: rs3130473; hg19: chr6-31199208;