rs16918758

Variant names:

• chr9-32879789-T-A
• rs16918758

Your query was ambiguous. Multiple possible variants found:

• chr9-32879789-T-A
• chr9-32879789-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.154 in 118,546 control chromosomes in the GnomAD database, including 1,915 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 0.15 (1915 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 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: 0.154 AC: 18238 AN: 118450 Hom.: 1919 Cov.: 31

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.0633

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.0652

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.154 AC: 18238 AN: 118546 Hom.: 1915 Cov.: 31 AF XY: 0.164 AC XY: 9519 AN XY: 57958

African (AFR) AF: 0.0492 AC: 1700 AN: 34564

American (AMR) AF: 0.317 AC: 3953 AN: 12476

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 283 AN: 2754

East Asian (EAS) AF: 0.536 AC: 2576 AN: 4802

South Asian (SAS) AF: 0.132 AC: 467 AN: 3548

European-Finnish (FIN) AF: 0.252 AC: 2015 AN: 8002

Middle Eastern (MID) AF: 0.0607 AC: 13 AN: 214

European-Non Finnish (NFE) AF: 0.139 AC: 6959 AN: 49956

Other (OTH) AF: 0.147 AC: 230 AN: 1566

Alfa AF: 0.110 Hom.: 155

Bravo AF: 0.127

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs16918758; hg19: chr9-32879787; COSMIC: COSV69459860;