rs9710693

chr2-238813613-T-Cchr2-238813613-T-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 0.645 in 151,960 control chromosomes in the GnomAD database, including 32,569 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 0.64 (32569 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.725 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: 0.645 AC: 97940 AN: 151842 Hom.: 32558 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.645 AC: 97996 AN: 151960 Hom.: 32569 Cov.: 31 AF XY: 0.637 AC XY: 47287 AN XY: 74246

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.678

Alfa AF: 0.707 Hom.: 53790

Bravo AF: 0.633

Asia WGS AF: 0.462 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.2
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9710693; hg19: chr2-239722254;