rs17094273

chr14-96637470-G-A

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 0.149 in 152,150 control chromosomes in the GnomAD database, including 2,068 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 0.15 (2068 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 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: 0.149 AC: 22584 AN: 152030 Hom.: 2063 Cov.: 34

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0950

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.149 AC: 22630 AN: 152150 Hom.: 2068 Cov.: 34 AF XY: 0.148 AC XY: 10972 AN XY: 74376

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0833

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.0950

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.145

Alfa AF: 0.112 Hom.: 1640

Bravo AF: 0.152

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.41
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17094273; hg19: chr14-97103807;