rs17799612

Variant names:

• chr4-31935842-G-A
• rs17799612

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 0.0665 in 151,754 control chromosomes in the GnomAD database, including 369 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 0.066 (369 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

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 = 0.0849 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: 0.0664 AC: 10076 AN: 151636 Hom.: 368 Cov.: 32

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0379

Gnomad EAS AF: 0.00847

Gnomad SAS AF: 0.0522

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.0629

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

GnomAD4 genome AF: 0.0665 AC: 10086 AN: 151754 Hom.: 369 Cov.: 32 AF XY: 0.0633 AC XY: 4694 AN XY: 74160

Gnomad4 AFR AF: 0.0523

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.0379

Gnomad4 EAS AF: 0.00849

Gnomad4 SAS AF: 0.0525

Gnomad4 FIN AF: 0.0457

Gnomad4 NFE AF: 0.0868

Gnomad4 OTH AF: 0.0642

Alfa AF: 0.0800 Hom.: 242

Bravo AF: 0.0652

Asia WGS AF: 0.0310 AC: 111 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	1.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17799612; hg19: chr4-31937464;