rs17799805

Variant names:

• chr6-79399614-T-G
• rs17799805

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0857 in 152,184 control chromosomes in the GnomAD database, including 607 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 0.086 (607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.118 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: 0.0858 AC: 13040 AN: 152066 Hom.: 607 Cov.: 32

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0857 AC: 13037 AN: 152184 Hom.: 607 Cov.: 32 AF XY: 0.0837 AC XY: 6226 AN XY: 74400

African (AFR) AF: 0.0467 AC: 1941 AN: 41526

American (AMR) AF: 0.0902 AC: 1379 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3466

East Asian (EAS) AF: 0.101 AC: 523 AN: 5170

South Asian (SAS) AF: 0.126 AC: 607 AN: 4806

European-Finnish (FIN) AF: 0.0517 AC: 549 AN: 10610

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7191 AN: 68008

Other (OTH) AF: 0.110 AC: 232 AN: 2112

Alfa AF: 0.0968 Hom.: 123

Bravo AF: 0.0863

Asia WGS AF: 0.108 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.4
DANN	Benign	0.71
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs17799805; hg19: chr6-80109331;