14-28663671-G-A

Variant names:

• chr14-28663671-G-A
• rs1956388

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 0.49 in 151,732 control chromosomes in the GnomAD database, including 18,264 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 0.49 (18264 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74236 AN: 151614 Hom.: 18226 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.490 AC: 74332 AN: 151732 Hom.: 18264 Cov.: 32 AF XY: 0.494 AC XY: 36595 AN XY: 74102

African (AFR) AF: 0.526 AC: 21769 AN: 41390

American (AMR) AF: 0.543 AC: 8265 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3468

East Asian (EAS) AF: 0.505 AC: 2596 AN: 5142

South Asian (SAS) AF: 0.596 AC: 2876 AN: 4822

European-Finnish (FIN) AF: 0.436 AC: 4578 AN: 10504

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30921 AN: 67884

Other (OTH) AF: 0.491 AC: 1033 AN: 2104

Alfa AF: 0.464 Hom.: 45848

Bravo AF: 0.497

Asia WGS AF: 0.559 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.33
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1956388; hg19: chr14-29132877;