rs1150500

chr2-72894314-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0828

Gnomad4 ASJ AF: 0.0461

Gnomad4 EAS AF: 0.00598

Gnomad4 SAS AF: 0.0603

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0933

Gnomad4 OTH AF: 0.122

Alfa AF: 0.101 Hom.: 280

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1150500; hg19: chr2-73121443;