rs1150144

Variant names:

• chr2-156321991-G-A
• rs1150144

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 0.573 in 151,864 control chromosomes in the GnomAD database, including 27,024 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 0.57 (27024 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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: 0.574 AC: 87070 AN: 151744 Hom.: 27017 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.573 AC: 87088 AN: 151864 Hom.: 27024 Cov.: 31 AF XY: 0.575 AC XY: 42653 AN XY: 74222

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.616

Alfa AF: 0.670 Hom.: 33449

Bravo AF: 0.539

Asia WGS AF: 0.553 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	11
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1150144; hg19: chr2-157178503;