rs17496908

Variant names:

• chr2-44033208-A-G
• rs17496908

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 0.121 in 152,178 control chromosomes in the GnomAD database, including 1,427 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 0.12 (1427 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18440 AN: 152060 Hom.: 1430 Cov.: 32

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0741

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.121 AC: 18434 AN: 152178 Hom.: 1427 Cov.: 32 AF XY: 0.122 AC XY: 9081 AN XY: 74394

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0743

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.122

Alfa AF: 0.159 Hom.: 1937

Bravo AF: 0.112

Asia WGS AF: 0.0960 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	13
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17496908; hg19: chr2-44260347;