14-82119980-A-G

Variant names:

• chr14-82119980-A-G
• rs1652605

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.531 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

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.540

Alfa AF: 0.546 Hom.: 14227

Bravo AF: 0.522

Asia WGS AF: 0.423 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1652605; hg19: chr14-82586324;