rs3104404

Variant names:

• chr6-32714397-C-A
• rs3104404

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 0.243 in 152,048 control chromosomes in the GnomAD database, including 5,161 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 0.24 (5161 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 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: 0.243 AC: 36868 AN: 151930 Hom.: 5159 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.243 AC: 36899 AN: 152048 Hom.: 5161 Cov.: 33 AF XY: 0.244 AC XY: 18162 AN XY: 74342

African (AFR) AF: 0.298 AC: 12356 AN: 41446

American (AMR) AF: 0.261 AC: 3987 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3466

East Asian (EAS) AF: 0.414 AC: 2145 AN: 5182

South Asian (SAS) AF: 0.477 AC: 2298 AN: 4818

European-Finnish (FIN) AF: 0.0888 AC: 939 AN: 10576

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13058 AN: 67972

Other (OTH) AF: 0.301 AC: 635 AN: 2110

Alfa AF: 0.208 Hom.: 10700

Asia WGS AF: 0.475 AC: 1649 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	14
DANN	Benign	0.34
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs3104404; hg19: chr6-32682174;