rs6474413

chr8-42695921-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.672

Alfa AF: 0.752 Hom.: 42901

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6474413; hg19: chr8-42551064;