rs1959429

Variant names:

• chr14-41434311-G-A
• rs1959429

Your query was ambiguous. Multiple possible variants found:

• chr14-41434311-G-A
• chr14-41434311-G-T

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 0.297 in 151,874 control chromosomes in the GnomAD database, including 7,225 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 0.30 (7225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 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: 0.297 AC: 45043 AN: 151756 Hom.: 7212 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.297 AC: 45095 AN: 151874 Hom.: 7225 Cov.: 32 AF XY: 0.300 AC XY: 22279 AN XY: 74194

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.262

Alfa AF: 0.227 Hom.: 2253

Bravo AF: 0.299

Asia WGS AF: 0.350 AC: 1215 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.29
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1959429; hg19: chr14-41903514;