rs2256842

chr7-118764554-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;