rs17799462

Variant names:

• chr6-79397403-T-C
• rs17799462

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;