rs1157595

Variant names:

• chr2-181884841-T-C
• rs1157595

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 0.413 in 151,912 control chromosomes in the GnomAD database, including 15,320 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 0.41 (15320 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.438
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 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: 0.413 AC: 62690 AN: 151794 Hom.: 15322 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.413 AC: 62684 AN: 151912 Hom.: 15320 Cov.: 32 AF XY: 0.416 AC XY: 30862 AN XY: 74268

African (AFR) AF: 0.155 AC: 6436 AN: 41490

American (AMR) AF: 0.393 AC: 5996 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3470

East Asian (EAS) AF: 0.641 AC: 3308 AN: 5162

South Asian (SAS) AF: 0.405 AC: 1956 AN: 4824

European-Finnish (FIN) AF: 0.634 AC: 6687 AN: 10540

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35709 AN: 67854

Other (OTH) AF: 0.400 AC: 845 AN: 2110

Alfa AF: 0.484 Hom.: 33091

Bravo AF: 0.385

Asia WGS AF: 0.452 AC: 1571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.72
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs1157595; hg19: chr2-182749568;