rs1150500

Variant names:

• chr2-72894314-G-A
• rs1150500

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 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

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;