rs17093348

chr14-60207772-G-Achr14-60207772-G-T

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 0.0825 in 152,212 control chromosomes in the GnomAD database, including 918 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 0.082 (918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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: 0.0821 AC: 12483 AN: 152092 Hom.: 896 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0702

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

GnomAD4 genome AF: 0.0825 AC: 12556 AN: 152212 Hom.: 918 Cov.: 32 AF XY: 0.0824 AC XY: 6130 AN XY: 74432

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0903

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0162

Gnomad4 NFE AF: 0.0330

Gnomad4 OTH AF: 0.0723

Alfa AF: 0.0478 Hom.: 79

Bravo AF: 0.0883

Asia WGS AF: 0.144 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.77
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17093348; hg19: chr14-60674490;