rs1150144

Variant names:

• chr2-156321991-G-A
• rs1150144

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 0.573 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.339 AC: 14026 AN: 41334

American (AMR) AF: 0.518 AC: 7907 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2570 AN: 3466

East Asian (EAS) AF: 0.435 AC: 2243 AN: 5160

South Asian (SAS) AF: 0.601 AC: 2890 AN: 4812

European-Finnish (FIN) AF: 0.725 AC: 7661 AN: 10562

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47699 AN: 67952

Other (OTH) AF: 0.616 AC: 1299 AN: 2108

Alfa AF: 0.652 Hom.: 42274

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
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs1150144; hg19: chr2-157178503;