rs159153

chr3-9748191-T-C

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 0.319 in 152,150 control chromosomes in the GnomAD database, including 7,953 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 0.32 (7953 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

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 (AFR) allele frequency at 95% confidence interval = 0.354 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: 0.318 AC: 48394 AN: 152032 Hom.: 7911 Cov.: 33

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0960

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.319 AC: 48503 AN: 152150 Hom.: 7953 Cov.: 33 AF XY: 0.319 AC XY: 23741 AN XY: 74384

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0962

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.321

Alfa AF: 0.320 Hom.: 3099

Bravo AF: 0.318

Asia WGS AF: 0.263 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.7
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs159153; hg19: chr3-9789875;