chr2-181452475-A-T

Variant names:

• chr2-181452475-A-T
• rs155141

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 0.879 in 152,186 control chromosomes in the GnomAD database, including 58,841 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 0.88 (58841 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.884 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: 0.879 AC: 133626 AN: 152068 Hom.: 58794 Cov.: 31

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.879 AC: 133731 AN: 152186 Hom.: 58841 Cov.: 31 AF XY: 0.881 AC XY: 65545 AN XY: 74424

African (AFR) AF: 0.867 AC: 36016 AN: 41542

American (AMR) AF: 0.896 AC: 13692 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3023 AN: 3470

East Asian (EAS) AF: 0.794 AC: 4117 AN: 5182

South Asian (SAS) AF: 0.871 AC: 4200 AN: 4820

European-Finnish (FIN) AF: 0.929 AC: 9859 AN: 10612

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59824 AN: 67966

Other (OTH) AF: 0.872 AC: 1839 AN: 2108

Alfa AF: 0.879 Hom.: 7364

Bravo AF: 0.876

Asia WGS AF: 0.838 AC: 2917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.74
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs155141; hg19: chr2-182317202;