rs17043185

Positions:

• chr2-52669764-G-A

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 0.112 in 152,094 control chromosomes in the GnomAD database, including 1,881 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 (1881 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 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: 0.112 AC: 16994 AN: 151976 Hom.: 1877 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0853

Gnomad ASJ AF: 0.0230

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.0915

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

GnomAD4 genome AF: 0.112 AC: 17024 AN: 152094 Hom.: 1881 Cov.: 32 AF XY: 0.113 AC XY: 8420 AN XY: 74352

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.0854

Gnomad4 ASJ AF: 0.0230

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.0426

Gnomad4 NFE AF: 0.0298

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.0447 Hom.: 367

Bravo AF: 0.118

Asia WGS AF: 0.183 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17043185; hg19: chr2-52896902;