2-6461298-T-A

Variant names:

• chr2-6461298-T-A
• rs10929436

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 0.432 in 151,926 control chromosomes in the GnomAD database, including 15,308 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 0.43 (15308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65646 AN: 151808 Hom.: 15306 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.432 AC: 65674 AN: 151926 Hom.: 15308 Cov.: 32 AF XY: 0.443 AC XY: 32935 AN XY: 74270

African (AFR) AF: 0.267 AC: 11078 AN: 41456

American (AMR) AF: 0.536 AC: 8182 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1382 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2774 AN: 5166

South Asian (SAS) AF: 0.547 AC: 2629 AN: 4808

European-Finnish (FIN) AF: 0.671 AC: 7081 AN: 10552

Middle Eastern (MID) AF: 0.255 AC: 74 AN: 290

European-Non Finnish (NFE) AF: 0.458 AC: 31062 AN: 67884

Other (OTH) AF: 0.414 AC: 874 AN: 2112

Alfa AF: 0.442 Hom.: 1897

Bravo AF: 0.415

Asia WGS AF: 0.553 AC: 1923 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.57
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs10929436; hg19: chr2-6601430;