rs945658

Variant names:

• chr9-1616639-T-G
• rs945658

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 0.503 in 151,964 control chromosomes in the GnomAD database, including 20,026 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 0.50 (20026 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

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 = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76457 AN: 151844 Hom.: 20017 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.503 AC: 76499 AN: 151964 Hom.: 20026 Cov.: 32 AF XY: 0.509 AC XY: 37834 AN XY: 74286

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.499

Alfa AF: 0.507 Hom.: 5645

Bravo AF: 0.498

Asia WGS AF: 0.603 AC: 2096 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	2.5
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: rs945658; hg19: chr9-1616639; COSMIC: COSV69441158;