8-40524962-T-C

Variant names:

• chr8-40524962-T-C
• rs2589916

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;