18-2491876-A-C

Variant names:

• chr18-2491876-A-C
• rs2677906

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 0.743 in 152,206 control chromosomes in the GnomAD database, including 42,065 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 0.74 (42065 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112938 AN: 152088 Hom.: 42016 Cov.: 34

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.743 AC: 113045 AN: 152206 Hom.: 42065 Cov.: 34 AF XY: 0.740 AC XY: 55050 AN XY: 74404

African (AFR) AF: 0.788 AC: 32723 AN: 41526

American (AMR) AF: 0.693 AC: 10596 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2442 AN: 3472

East Asian (EAS) AF: 0.842 AC: 4370 AN: 5188

South Asian (SAS) AF: 0.659 AC: 3179 AN: 4822

European-Finnish (FIN) AF: 0.711 AC: 7523 AN: 10582

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49900 AN: 67996

Other (OTH) AF: 0.745 AC: 1575 AN: 2114

Alfa AF: 0.734 Hom.: 111596

Bravo AF: 0.743

Asia WGS AF: 0.728 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.51
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2677906; hg19: chr18-2491875;