rs2256842

Variant names:

• chr7-118764554-A-G
• rs2256842

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 0.106 in 152,148 control chromosomes in the GnomAD database, including 2,569 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 0.11 (2569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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: 0.106 AC: 16047 AN: 152030 Hom.: 2559 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0100

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00975

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.106 AC: 16089 AN: 152148 Hom.: 2569 Cov.: 32 AF XY: 0.102 AC XY: 7582 AN XY: 74398

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.0444

Gnomad4 ASJ AF: 0.00864

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.0100

Gnomad4 NFE AF: 0.00973

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0681 Hom.: 191

Bravo AF: 0.118

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256842; hg19: chr7-118404608;