14-41434311-G-A

Variant names:

• chr14-41434311-G-A
• rs1959429
• ENST00000787890.1:n.53-54426G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000787890.1(ENSG00000302567):​n.53-54426G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000302567 ENST00000787890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 5 publications found

Genes affected

ENSG00000302567 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000302567	ENST00000787890.1	n.53-54426G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.400 AC: 16588 AN: 41432

American (AMR) AF: 0.276 AC: 4210 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 916 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2165 AN: 5140

South Asian (SAS) AF: 0.224 AC: 1082 AN: 4830

European-Finnish (FIN) AF: 0.288 AC: 3041 AN: 10560

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16051 AN: 67892

Other (OTH) AF: 0.262 AC: 554 AN: 2112

Alfa AF: 0.235 Hom.: 3277

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1959429; hg19: chr14-41903514;