rs2989727

Variant names:

• chr9-134919852-C-T
• rs2989727

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 0.567 in 152,094 control chromosomes in the GnomAD database, including 24,893 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 0.57 (24893 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 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: 0.567 AC: 86238 AN: 151976 Hom.: 24892 Cov.: 34

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.567 AC: 86270 AN: 152094 Hom.: 24893 Cov.: 34 AF XY: 0.569 AC XY: 42337 AN XY: 74350

African (AFR) AF: 0.490 AC: 20332 AN: 41478

American (AMR) AF: 0.475 AC: 7256 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3472

East Asian (EAS) AF: 0.429 AC: 2220 AN: 5170

South Asian (SAS) AF: 0.574 AC: 2770 AN: 4826

European-Finnish (FIN) AF: 0.659 AC: 6960 AN: 10568

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42510 AN: 67978

Other (OTH) AF: 0.550 AC: 1160 AN: 2110

Alfa AF: 0.606 Hom.: 14480

Bravo AF: 0.545

Asia WGS AF: 0.475 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.43
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2989727; hg19: chr9-137811698;