8-40043200-T-C

Variant names:

• chr8-40043200-T-C
• rs2929116

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 0.91 in 152,312 control chromosomes in the GnomAD database, including 63,181 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 0.91 (63181 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.910 AC: 138475 AN: 152194 Hom.: 63135 Cov.: 33

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.910 AC: 138575 AN: 152312 Hom.: 63181 Cov.: 33 AF XY: 0.911 AC XY: 67828 AN XY: 74480

African (AFR) AF: 0.920 AC: 38227 AN: 41560

American (AMR) AF: 0.829 AC: 12683 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.943 AC: 3271 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5145 AN: 5178

South Asian (SAS) AF: 0.980 AC: 4734 AN: 4832

European-Finnish (FIN) AF: 0.902 AC: 9576 AN: 10614

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61861 AN: 68032

Other (OTH) AF: 0.913 AC: 1931 AN: 2116

Alfa AF: 0.900 Hom.: 15579

Bravo AF: 0.899

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2929116; hg19: chr8-39900719;