chr2-137727463-G-A

Variant names:

• chr2-137727463-G-A
• rs1446224

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 0.157 in 135,116 control chromosomes in the GnomAD database, including 2,889 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 0.16 (2889 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.920
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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: 0.157 AC: 21204 AN: 134988 Hom.: 2872 Cov.: 30

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0474

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.157 AC: 21266 AN: 135116 Hom.: 2889 Cov.: 30 AF XY: 0.160 AC XY: 10634 AN XY: 66572

African (AFR) AF: 0.327 AC: 12763 AN: 39066

American (AMR) AF: 0.231 AC: 3168 AN: 13690

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 135 AN: 3040

East Asian (EAS) AF: 0.494 AC: 2394 AN: 4848

South Asian (SAS) AF: 0.139 AC: 558 AN: 4028

European-Finnish (FIN) AF: 0.0254 AC: 242 AN: 9536

Middle Eastern (MID) AF: 0.114 AC: 29 AN: 254

European-Non Finnish (NFE) AF: 0.0289 AC: 1676 AN: 58034

Other (OTH) AF: 0.143 AC: 264 AN: 1840

Alfa AF: 0.0827 Hom.: 183

Bravo AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.66
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1446224; hg19: chr2-138485033;