rs155141

chr2-181452475-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.872

Alfa AF: 0.878 Hom.: 5415

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs155141; hg19: chr2-182317202;