14-46778772-T-A

Variant names:

• chr14-46778772-T-A
• rs1532202

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 0.536 in 151,506 control chromosomes in the GnomAD database, including 22,775 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 0.54 (22775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.748
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81129 AN: 151388 Hom.: 22745 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.536 AC: 81207 AN: 151506 Hom.: 22775 Cov.: 32 AF XY: 0.535 AC XY: 39589 AN XY: 74022

African (AFR) AF: 0.680 AC: 28169 AN: 41412

American (AMR) AF: 0.331 AC: 5031 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3466

East Asian (EAS) AF: 0.389 AC: 2006 AN: 5160

South Asian (SAS) AF: 0.610 AC: 2942 AN: 4822

European-Finnish (FIN) AF: 0.568 AC: 5987 AN: 10534

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33655 AN: 67620

Other (OTH) AF: 0.477 AC: 1003 AN: 2102

Alfa AF: 0.516 Hom.: 2585

Bravo AF: 0.519

Asia WGS AF: 0.573 AC: 1992 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.7
DANN	Benign	0.51
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs1532202; hg19: chr14-47247975;