rs17096179

Variant names:

• chr14-59372049-A-C
• rs17096179

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 0.134 in 152,160 control chromosomes in the GnomAD database, including 1,840 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 0.13 (1840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 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: 0.134 AC: 20352 AN: 152042 Hom.: 1837 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.134 AC: 20369 AN: 152160 Hom.: 1840 Cov.: 32 AF XY: 0.130 AC XY: 9672 AN XY: 74406

African (AFR) AF: 0.260 AC: 10791 AN: 41486

American (AMR) AF: 0.100 AC: 1530 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4826

European-Finnish (FIN) AF: 0.0921 AC: 976 AN: 10598

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0896 AC: 6091 AN: 67998

Other (OTH) AF: 0.128 AC: 270 AN: 2114

Alfa AF: 0.108 Hom.: 1511

Bravo AF: 0.142

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.13
DANN	Benign	0.69
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs17096179; hg19: chr14-59838767;