chr8-96357406-C-A

Variant names:

• chr8-96357406-C-A
• rs2640806

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 0.404 in 151,968 control chromosomes in the GnomAD database, including 12,892 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 0.40 (12892 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.404 AC: 61302 AN: 151850 Hom.: 12877 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.404 AC: 61349 AN: 151968 Hom.: 12892 Cov.: 32 AF XY: 0.400 AC XY: 29687 AN XY: 74280

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.0940

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.377

Alfa AF: 0.411 Hom.: 25886

Bravo AF: 0.403

Asia WGS AF: 0.215 AC: 750 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2640806; hg19: chr8-97369634;