chr2-180497009-T-A

Variant names:

• chr2-180497009-T-A
• rs1157535

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 0.296 in 152,084 control chromosomes in the GnomAD database, including 7,010 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 0.30 (7010 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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: 0.295 AC: 44882 AN: 151964 Hom.: 6985 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.296 AC: 44952 AN: 152084 Hom.: 7010 Cov.: 32 AF XY: 0.301 AC XY: 22406 AN XY: 74332

African (AFR) AF: 0.233 AC: 9666 AN: 41490

American (AMR) AF: 0.385 AC: 5892 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3468

East Asian (EAS) AF: 0.471 AC: 2429 AN: 5158

South Asian (SAS) AF: 0.433 AC: 2087 AN: 4820

European-Finnish (FIN) AF: 0.328 AC: 3465 AN: 10564

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19530 AN: 67982

Other (OTH) AF: 0.267 AC: 563 AN: 2108

Alfa AF: 0.183 Hom.: 408

Bravo AF: 0.292

Asia WGS AF: 0.468 AC: 1623 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.2
DANN	Benign	0.85
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1157535; hg19: chr2-181361736;