rs9890008

chr17-14568376-A-Gchr17-14568376-A-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 0.727 in 152,072 control chromosomes in the GnomAD database, including 40,379 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 0.73 (40379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

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 (AMR) allele frequency at 95% confidence interval = 0.781 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: 0.727 AC: 110436 AN: 151952 Hom.: 40360 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.727 AC: 110504 AN: 152072 Hom.: 40379 Cov.: 32 AF XY: 0.722 AC XY: 53654 AN XY: 74320

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.736

Alfa AF: 0.733 Hom.: 20887

Bravo AF: 0.740

Asia WGS AF: 0.633 AC: 2204 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	1.8
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9890008; hg19: chr17-14471693;