8-40954078-C-T

Variant names:

• chr8-40954078-C-T
• rs907561

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.827 AC: 34340 AN: 41522

American (AMR) AF: 0.757 AC: 11564 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2291 AN: 3468

East Asian (EAS) AF: 0.757 AC: 3904 AN: 5158

South Asian (SAS) AF: 0.777 AC: 3747 AN: 4820

European-Finnish (FIN) AF: 0.757 AC: 8000 AN: 10572

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49197 AN: 67972

Other (OTH) AF: 0.726 AC: 1534 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.16
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs907561; hg19: chr8-40811597;