14-82119980-A-G

Variant names:

• chr14-82119980-A-G
• rs1652605

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 0.531 in 151,558 control chromosomes in the GnomAD database, including 21,758 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 0.53 (21758 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.893
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 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: 0.531 AC: 80429 AN: 151440 Hom.: 21732 Cov.: 31

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.531 AC: 80510 AN: 151558 Hom.: 21758 Cov.: 31 AF XY: 0.526 AC XY: 38940 AN XY: 74040

African (AFR) AF: 0.523 AC: 21625 AN: 41328

American (AMR) AF: 0.437 AC: 6632 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1629 AN: 3460

East Asian (EAS) AF: 0.392 AC: 2006 AN: 5112

South Asian (SAS) AF: 0.413 AC: 1985 AN: 4812

European-Finnish (FIN) AF: 0.563 AC: 5945 AN: 10568

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38819 AN: 67786

Other (OTH) AF: 0.540 AC: 1135 AN: 2102

Alfa AF: 0.544 Hom.: 19086

Bravo AF: 0.522

Asia WGS AF: 0.423 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.2
DANN	Benign	0.44
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs1652605; hg19: chr14-82586324;