rs1958666

Variant names:

• chr14-82183056-C-A
• rs1958666

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 0.459 in 151,506 control chromosomes in the GnomAD database, including 16,463 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 0.46 (16463 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 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: 0.459 AC: 69545 AN: 151384 Hom.: 16452 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.459 AC: 69608 AN: 151506 Hom.: 16463 Cov.: 31 AF XY: 0.456 AC XY: 33732 AN XY: 74004

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.473

Alfa AF: 0.495 Hom.: 8645

Bravo AF: 0.448

Asia WGS AF: 0.402 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1958666; hg19: chr14-82649400;