chr2-2336876-T-C

Variant names:

• chr2-2336876-T-C
• rs10495487

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 0.0658 in 152,322 control chromosomes in the GnomAD database, including 446 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 0.066 (446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0992 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: 0.0659 AC: 10023 AN: 152204 Hom.: 447 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0658 AC: 10018 AN: 152322 Hom.: 446 Cov.: 32 AF XY: 0.0632 AC XY: 4707 AN XY: 74494

African (AFR) AF: 0.0202 AC: 838 AN: 41588

American (AMR) AF: 0.0515 AC: 787 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0248 AC: 120 AN: 4830

European-Finnish (FIN) AF: 0.0786 AC: 834 AN: 10614

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6885 AN: 68030

Other (OTH) AF: 0.0540 AC: 114 AN: 2112

Alfa AF: 0.0902 Hom.: 1115

Bravo AF: 0.0628

Asia WGS AF: 0.0100 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.079
DANN	Benign	0.56
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10495487; hg19: chr2-2340648;