rs17799462

chr6-79397403-T-C

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 0.0722 in 152,222 control chromosomes in the GnomAD database, including 425 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 0.072 (425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 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: 0.0723 AC: 10994 AN: 152104 Hom.: 425 Cov.: 32

Gnomad AFR AF: 0.0376

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0477

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.0958

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

GnomAD4 genome AF: 0.0722 AC: 10993 AN: 152222 Hom.: 425 Cov.: 32 AF XY: 0.0709 AC XY: 5277 AN XY: 74404

Gnomad4 AFR AF: 0.0376

Gnomad4 AMR AF: 0.0777

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0477

Gnomad4 NFE AF: 0.0871

Gnomad4 OTH AF: 0.0962

Alfa AF: 0.0835 Hom.: 77

Bravo AF: 0.0727

Asia WGS AF: 0.105 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.076
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17799462; hg19: chr6-80107120;