3-27747289-C-T

Variant names:

• chr3-27747289-C-T
• rs11129295

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 0.4 in 152,008 control chromosomes in the GnomAD database, including 13,245 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 0.40 (13245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 53 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 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: 0.400 AC: 60717 AN: 151890 Hom.: 13229 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.400 AC: 60764 AN: 152008 Hom.: 13245 Cov.: 32 AF XY: 0.408 AC XY: 30292 AN XY: 74292

African (AFR) AF: 0.325 AC: 13476 AN: 41452

American (AMR) AF: 0.557 AC: 8498 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1511 AN: 3468

East Asian (EAS) AF: 0.768 AC: 3965 AN: 5166

South Asian (SAS) AF: 0.665 AC: 3201 AN: 4816

European-Finnish (FIN) AF: 0.356 AC: 3757 AN: 10562

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.369 AC: 25077 AN: 67954

Other (OTH) AF: 0.422 AC: 893 AN: 2116

Alfa AF: 0.390 Hom.: 55111

Bravo AF: 0.409

Asia WGS AF: 0.688 AC: 2391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs11129295; hg19: chr3-27788780;