2-150768368-C-T

Variant names:

• chr2-150768368-C-T
• rs6734792

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.551 in 152,082 control chromosomes in the GnomAD database, including 23,546 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 0.55 (23546 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.641 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: 0.551 AC: 83756 AN: 151964 Hom.: 23532 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.551 AC: 83803 AN: 152082 Hom.: 23546 Cov.: 33 AF XY: 0.545 AC XY: 40550 AN XY: 74340

African (AFR) AF: 0.463 AC: 19187 AN: 41484

American (AMR) AF: 0.652 AC: 9950 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1820 AN: 3470

East Asian (EAS) AF: 0.582 AC: 3015 AN: 5178

South Asian (SAS) AF: 0.586 AC: 2824 AN: 4822

European-Finnish (FIN) AF: 0.449 AC: 4743 AN: 10570

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40277 AN: 67974

Other (OTH) AF: 0.558 AC: 1179 AN: 2114

Alfa AF: 0.581 Hom.: 81642

Bravo AF: 0.563

Asia WGS AF: 0.588 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	16
DANN	Benign	0.58
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs6734792; hg19: chr2-151624882;