rs6474413

Variant names:

• chr8-42695921-C-T
• rs6474413

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 0.638 in 152,134 control chromosomes in the GnomAD database, including 34,311 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 0.64 (34311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 27 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 (EAS) allele frequency at 95% confidence interval = 0.786 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: 0.639 AC: 97102 AN: 152014 Hom.: 34301 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.638 AC: 97135 AN: 152134 Hom.: 34311 Cov.: 32 AF XY: 0.643 AC XY: 47844 AN XY: 74372

African (AFR) AF: 0.311 AC: 12887 AN: 41496

American (AMR) AF: 0.713 AC: 10900 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2447 AN: 3466

East Asian (EAS) AF: 0.807 AC: 4178 AN: 5180

South Asian (SAS) AF: 0.712 AC: 3425 AN: 4812

European-Finnish (FIN) AF: 0.760 AC: 8044 AN: 10590

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52880 AN: 67990

Other (OTH) AF: 0.672 AC: 1421 AN: 2116

Alfa AF: 0.737 Hom.: 60197

Bravo AF: 0.619

Asia WGS AF: 0.707 AC: 2458 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	1.0
DANN	Benign	0.35
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs6474413; hg19: chr8-42551064;