rs2049040

Variant names:

• chr9-137002712-C-T
• rs2049040

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 0.71 in 152,202 control chromosomes in the GnomAD database, including 38,581 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 0.71 (38581 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 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: 0.710 AC: 107985 AN: 152084 Hom.: 38552 Cov.: 34

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.710 AC: 108068 AN: 152202 Hom.: 38581 Cov.: 34 AF XY: 0.709 AC XY: 52760 AN XY: 74432

African (AFR) AF: 0.772 AC: 32080 AN: 41534

American (AMR) AF: 0.632 AC: 9658 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2460 AN: 3472

East Asian (EAS) AF: 0.811 AC: 4208 AN: 5190

South Asian (SAS) AF: 0.776 AC: 3741 AN: 4822

European-Finnish (FIN) AF: 0.639 AC: 6751 AN: 10568

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46805 AN: 68010

Other (OTH) AF: 0.713 AC: 1505 AN: 2110

Alfa AF: 0.694 Hom.: 6666

Bravo AF: 0.711

Asia WGS AF: 0.770 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.69
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2049040; hg19: chr9-139897164;