2-145287997-A-T

Variant names:

• chr2-145287997-A-T
• rs11687420

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.283 in 151,490 control chromosomes in the GnomAD database, including 6,235 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 0.28 (6235 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.82
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 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: 0.283 AC: 42814 AN: 151372 Hom.: 6236 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.283 AC: 42817 AN: 151490 Hom.: 6235 Cov.: 31 AF XY: 0.281 AC XY: 20804 AN XY: 74002

African (AFR) AF: 0.257 AC: 10637 AN: 41352

American (AMR) AF: 0.292 AC: 4422 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1156 AN: 3462

East Asian (EAS) AF: 0.118 AC: 602 AN: 5114

South Asian (SAS) AF: 0.306 AC: 1475 AN: 4816

European-Finnish (FIN) AF: 0.274 AC: 2896 AN: 10556

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.306 AC: 20731 AN: 67724

Other (OTH) AF: 0.285 AC: 598 AN: 2100

Alfa AF: 0.303 Hom.: 874

Bravo AF: 0.280

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Benign	0.82
PhyloP100		3.8

Splicing

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

Other links and lift over

dbSNP: rs11687420; hg19: chr2-146045565;