chr2-72894314-G-A

Variant names:

• chr2-72894314-G-A
• rs1150500

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 0.115 in 152,288 control chromosomes in the GnomAD database, including 1,304 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 0.12 (1304 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 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: 0.115 AC: 17491 AN: 152170 Hom.: 1293 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0933

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.115 AC: 17529 AN: 152288 Hom.: 1304 Cov.: 33 AF XY: 0.111 AC XY: 8234 AN XY: 74478

African (AFR) AF: 0.205 AC: 8499 AN: 41540

American (AMR) AF: 0.0828 AC: 1266 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0461 AC: 160 AN: 3472

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5186

South Asian (SAS) AF: 0.0603 AC: 291 AN: 4828

European-Finnish (FIN) AF: 0.0519 AC: 551 AN: 10620

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0933 AC: 6345 AN: 68024

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.103 Hom.: 348

Bravo AF: 0.123

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.43
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1150500; hg19: chr2-73121443;