8-40524962-T-C

Position:

• chr8-40524962-T-C

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 0.61 in 152,148 control chromosomes in the GnomAD database, including 29,047 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 0.61 (29047 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 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: 0.610 AC: 92807 AN: 152030 Hom.: 29028 Cov.: 34

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.610 AC: 92865 AN: 152148 Hom.: 29047 Cov.: 34 AF XY: 0.613 AC XY: 45626 AN XY: 74380

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.623

Alfa AF: 0.533 Hom.: 1717

Bravo AF: 0.600

Asia WGS AF: 0.604 AC: 2099 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.10
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2589916; hg19: chr8-40382481;