2-183061038-C-T

Variant names:

• chr2-183061038-C-T
• rs2675073

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 0.926 in 152,208 control chromosomes in the GnomAD database, including 65,356 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 0.93 (65356 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.926 AC: 140888 AN: 152090 Hom.: 65300 Cov.: 31

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.926 AC: 141002 AN: 152208 Hom.: 65356 Cov.: 31 AF XY: 0.929 AC XY: 69094 AN XY: 74402

African (AFR) AF: 0.902 AC: 37457 AN: 41518

American (AMR) AF: 0.936 AC: 14309 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3028 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5149 AN: 5156

South Asian (SAS) AF: 0.965 AC: 4648 AN: 4816

European-Finnish (FIN) AF: 0.964 AC: 10229 AN: 10614

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63107 AN: 68034

Other (OTH) AF: 0.929 AC: 1959 AN: 2108

Alfa AF: 0.926 Hom.: 13248

Bravo AF: 0.923

Asia WGS AF: 0.980 AC: 3407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.45
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2675073; hg19: chr2-183925766;