rs17097373

Variant names:

• chr14-60360092-T-C
• rs17097373

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 0.0952 in 152,084 control chromosomes in the GnomAD database, including 1,062 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 0.095 (1062 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 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: 0.0951 AC: 14456 AN: 151964 Hom.: 1060 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0622

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.0224

Gnomad MID AF: 0.0822

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.0952 AC: 14475 AN: 152084 Hom.: 1062 Cov.: 32 AF XY: 0.0905 AC XY: 6728 AN XY: 74336

African (AFR) AF: 0.204 AC: 8476 AN: 41476

American (AMR) AF: 0.0621 AC: 948 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3470

East Asian (EAS) AF: 0.00366 AC: 19 AN: 5190

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4822

European-Finnish (FIN) AF: 0.0224 AC: 238 AN: 10604

Middle Eastern (MID) AF: 0.0880 AC: 25 AN: 284

European-Non Finnish (NFE) AF: 0.0606 AC: 4118 AN: 67940

Other (OTH) AF: 0.0946 AC: 200 AN: 2114

Alfa AF: 0.0732 Hom.: 410

Bravo AF: 0.105

Asia WGS AF: 0.0330 AC: 116 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.71
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs17097373; hg19: chr14-60826810;