rs945658

chr9-1616639-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;