chr8-53960651-T-C

Variant names:

• chr8-53960651-T-C
• rs7009781

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 0.385 in 151,870 control chromosomes in the GnomAD database, including 15,964 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 0.38 (15964 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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: 0.384 AC: 58328 AN: 151752 Hom.: 15909 Cov.: 31

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.385 AC: 58452 AN: 151870 Hom.: 15964 Cov.: 31 AF XY: 0.394 AC XY: 29265 AN XY: 74214

African (AFR) AF: 0.727 AC: 30126 AN: 41418

American (AMR) AF: 0.385 AC: 5863 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 925 AN: 3472

East Asian (EAS) AF: 0.744 AC: 3828 AN: 5148

South Asian (SAS) AF: 0.479 AC: 2293 AN: 4786

European-Finnish (FIN) AF: 0.311 AC: 3277 AN: 10540

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11025 AN: 67964

Other (OTH) AF: 0.363 AC: 765 AN: 2110

Alfa AF: 0.244 Hom.: 10115

Bravo AF: 0.405

Asia WGS AF: 0.623 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.72
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7009781; hg19: chr8-54873211;