rs2962896

Positions:

• chr5-18417974-A-G
• chr5-18417974-A-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 0.588 in 151,902 control chromosomes in the GnomAD database, including 27,013 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 0.59 (27013 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89340 AN: 151782 Hom.: 27030 Cov.: 31

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.588 AC: 89342 AN: 151902 Hom.: 27013 Cov.: 31 AF XY: 0.591 AC XY: 43851 AN XY: 74222

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.624

Alfa AF: 0.642 Hom.: 65236

Bravo AF: 0.564

Asia WGS AF: 0.516 AC: 1793 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
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: rs2962896; hg19: chr5-18418083;