chr8-56724674-G-A

Position:

• chr8-56724674-G-A

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 0.589 in 151,908 control chromosomes in the GnomAD database, including 27,615 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 0.59 (27615 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89412 AN: 151790 Hom.: 27577 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.589 AC: 89505 AN: 151908 Hom.: 27615 Cov.: 31 AF XY: 0.589 AC XY: 43735 AN XY: 74228

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.547

Alfa AF: 0.511 Hom.: 26927

Bravo AF: 0.591

Asia WGS AF: 0.739 AC: 2568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1834413; hg19: chr8-57637233;