rs17095330

Positions:

• chr14-97383563-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 0.256 in 152,078 control chromosomes in the GnomAD database, including 5,070 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 0.26 (5070 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 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: 0.256 AC: 38906 AN: 151960 Hom.: 5058 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.256 AC: 38970 AN: 152078 Hom.: 5070 Cov.: 32 AF XY: 0.254 AC XY: 18858 AN XY: 74310

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.288

Alfa AF: 0.243 Hom.: 711

Bravo AF: 0.259

Asia WGS AF: 0.237 AC: 820 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17095330; hg19: chr14-97849900;