rs2140913

chr7-113087998-C-Achr7-113087998-C-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 0.824 in 152,166 control chromosomes in the GnomAD database, including 51,811 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 0.82 (51811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 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: 0.824 AC: 125236 AN: 152048 Hom.: 51774 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.824 AC: 125324 AN: 152166 Hom.: 51811 Cov.: 32 AF XY: 0.824 AC XY: 61335 AN XY: 74414

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.820

Gnomad4 OTH AF: 0.835

Alfa AF: 0.823 Hom.: 49911

Bravo AF: 0.828

Asia WGS AF: 0.825 AC: 2865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.15
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2140913; hg19: chr7-112728053;