rs3130653

Variant names:

• chr6-30854994-C-A
• rs3130653

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 0.488 in 151,944 control chromosomes in the GnomAD database, including 19,059 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 0.49 (19059 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 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: 0.488 AC: 74155 AN: 151826 Hom.: 19046 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.488 AC: 74207 AN: 151944 Hom.: 19059 Cov.: 31 AF XY: 0.482 AC XY: 35792 AN XY: 74244

African (AFR) AF: 0.362 AC: 15021 AN: 41444

American (AMR) AF: 0.411 AC: 6277 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2193 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1696 AN: 5158

South Asian (SAS) AF: 0.381 AC: 1834 AN: 4808

European-Finnish (FIN) AF: 0.536 AC: 5652 AN: 10548

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39902 AN: 67944

Other (OTH) AF: 0.469 AC: 987 AN: 2104

Alfa AF: 0.556 Hom.: 57722

Bravo AF: 0.476

Asia WGS AF: 0.313 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.60
DANN	Benign	0.88
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3130653; hg19: chr6-30822771;