chr2-150646649-T-C

Variant names:

• chr2-150646649-T-C
• rs2341090

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 0.918 in 152,232 control chromosomes in the GnomAD database, including 64,217 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 0.92 (64217 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139650 AN: 152114 Hom.: 64159 Cov.: 32

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.918 AC: 139768 AN: 152232 Hom.: 64217 Cov.: 32 AF XY: 0.919 AC XY: 68373 AN XY: 74414

African (AFR) AF: 0.922 AC: 38292 AN: 41550

American (AMR) AF: 0.943 AC: 14406 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3092 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4537 AN: 5170

South Asian (SAS) AF: 0.962 AC: 4638 AN: 4820

European-Finnish (FIN) AF: 0.901 AC: 9544 AN: 10596

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.915 AC: 62247 AN: 68028

Other (OTH) AF: 0.916 AC: 1936 AN: 2114

Alfa AF: 0.920 Hom.: 7827

Bravo AF: 0.919

Asia WGS AF: 0.945 AC: 3281 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.8
DANN	Benign	0.79
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2341090; hg19: chr2-151503163;