8-40954078-C-T

Position:

• chr8-40954078-C-T

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 0.758 in 152,094 control chromosomes in the GnomAD database, including 43,945 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 0.76 (43945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 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: 0.758 AC: 115212 AN: 151976 Hom.: 43907 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.758 AC: 115299 AN: 152094 Hom.: 43945 Cov.: 32 AF XY: 0.758 AC XY: 56372 AN XY: 74326

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.726

Alfa AF: 0.710 Hom.: 3742

Bravo AF: 0.760

Asia WGS AF: 0.791 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs907561; hg19: chr8-40811597;