rs56342413

Variant names:

• chr8-6963986-C-A
• rs56342413

Your query was ambiguous. Multiple possible variants found:

• chr8-6963986-C-A
• chr8-6963986-C-T

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 0.0659 in 152,220 control chromosomes in the GnomAD database, including 458 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 0.066 (458 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 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: 0.0660 AC: 10032 AN: 152102 Hom.: 458 Cov.: 33

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0659 AC: 10029 AN: 152220 Hom.: 458 Cov.: 33 AF XY: 0.0628 AC XY: 4677 AN XY: 74430

African (AFR) AF: 0.0188 AC: 783 AN: 41548

American (AMR) AF: 0.0555 AC: 848 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.0183 AC: 88 AN: 4818

European-Finnish (FIN) AF: 0.0671 AC: 711 AN: 10600

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6941 AN: 68004

Other (OTH) AF: 0.0643 AC: 136 AN: 2114

Alfa AF: 0.0564 Hom.: 121

Bravo AF: 0.0635

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.84
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs56342413; hg19: chr8-6821508;