rs1150144

Positions:

• chr2-156321991-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 0.573 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;