2-5329700-T-C

Variant names:

• chr2-5329700-T-C
• rs6734151

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 0.646 in 152,076 control chromosomes in the GnomAD database, including 32,311 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 0.65 (32311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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: 0.646 AC: 98160 AN: 151960 Hom.: 32251 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.646 AC: 98284 AN: 152076 Hom.: 32311 Cov.: 32 AF XY: 0.649 AC XY: 48249 AN XY: 74340

African (AFR) AF: 0.751 AC: 31146 AN: 41480

American (AMR) AF: 0.700 AC: 10690 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2089 AN: 3464

East Asian (EAS) AF: 0.792 AC: 4087 AN: 5162

South Asian (SAS) AF: 0.592 AC: 2855 AN: 4824

European-Finnish (FIN) AF: 0.619 AC: 6545 AN: 10572

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38759 AN: 67980

Other (OTH) AF: 0.642 AC: 1355 AN: 2110

Alfa AF: 0.595 Hom.: 114610

Bravo AF: 0.660

Asia WGS AF: 0.697 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.65
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs6734151; hg19: chr2-5469833;