rs2656272

Variant names:

• chr8-54349340-G-A
• rs2656272

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 0.429 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.380

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2656272; hg19: chr8-55261900;