chr9-27581241-T-C

Variant names:

• chr9-27581241-T-C
• rs2783010

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.482 in 151,802 control chromosomes in the GnomAD database, including 17,748 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 0.48 (17748 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.629
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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: 0.482 AC: 73144 AN: 151682 Hom.: 17726 Cov.: 33

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.482 AC: 73211 AN: 151802 Hom.: 17748 Cov.: 33 AF XY: 0.482 AC XY: 35736 AN XY: 74210

African (AFR) AF: 0.532 AC: 21997 AN: 41362

American (AMR) AF: 0.467 AC: 7128 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1483 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2355 AN: 5162

South Asian (SAS) AF: 0.471 AC: 2269 AN: 4822

European-Finnish (FIN) AF: 0.450 AC: 4738 AN: 10520

Middle Eastern (MID) AF: 0.514 AC: 149 AN: 290

European-Non Finnish (NFE) AF: 0.465 AC: 31543 AN: 67896

Other (OTH) AF: 0.483 AC: 1019 AN: 2108

Alfa AF: 0.477 Hom.: 22938

Bravo AF: 0.490

Asia WGS AF: 0.469 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	11
DANN	Benign	0.55
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs2783010; hg19: chr9-27581239;