rs917235

chr2-75598693-G-Achr2-75598693-G-T

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 0.553 in 152,098 control chromosomes in the GnomAD database, including 23,420 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 0.55 (23407 hom., cov: 32)
  • Exomes 𝑓: 0.52 (13 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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: 0.553 AC: 84006 AN: 151890 Hom.: 23378 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.555

GnomAD4 exome AF: 0.522 AC: 47 AN: 90 Hom.: 13 AF XY: 0.533 AC XY: 32 AN XY: 60

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.700

Gnomad4 NFE exome AF: 0.548

Gnomad4 OTH exome AF: 0.214

GnomAD4 genome AF: 0.553 AC: 84098 AN: 152008 Hom.: 23407 Cov.: 32 AF XY: 0.556 AC XY: 41330 AN XY: 74314

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.555

Alfa AF: 0.529 Hom.: 43807

Bravo AF: 0.552

Asia WGS AF: 0.644 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	9.3
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs917235; hg19: chr2-75825819;