8-54349340-G-A

Variant names:

• chr8-54349340-G-A
• rs2656272

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 0.429 in 152,046 control chromosomes in the GnomAD database, including 15,190 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 0.43 (15190 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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: 0.429 AC: 65111 AN: 151932 Hom.: 15159 Cov.: 33

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.429 AC: 65196 AN: 152046 Hom.: 15190 Cov.: 33 AF XY: 0.427 AC XY: 31721 AN XY: 74320

African (AFR) AF: 0.620 AC: 25720 AN: 41460

American (AMR) AF: 0.313 AC: 4790 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2318 AN: 5174

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4822

European-Finnish (FIN) AF: 0.385 AC: 4066 AN: 10554

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.361 AC: 24509 AN: 67966

Other (OTH) AF: 0.380 AC: 804 AN: 2114

Alfa AF: 0.390 Hom.: 2115

Bravo AF: 0.428

Asia WGS AF: 0.401 AC: 1393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.037
DANN	Benign	0.64
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2656272; hg19: chr8-55261900;