rs17799612

chr4-31935842-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 0.0665 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;