14-39672210-T-C

Variant names:

• chr14-39672210-T-C
• rs1950634
• ENST00000650911.1:n.417+16402T>C

Variant summary

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

The ENST00000650911.1(ENSG00000258526):​n.417+16402T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,886 control chromosomes in the GnomAD database, including 25,383 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 0.55 (25383 hom., cov: 32)
• Consequence: ENSG00000258526 ENST00000650911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 2 publications found

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370461	XR_001750719.2	n.548+16402T>C		intron_variant	Intron 4 of 4
LOC105370461	XR_001750722.2	n.496+16402T>C		intron_variant	Intron 3 of 3
LOC105370461	XR_001750723.2	n.567+16402T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258526	ENST00000650911.1	n.417+16402T>C		intron_variant	Intron 3 of 5
ENSG00000258526	ENST00000651829.1	n.1196+16402T>C		intron_variant	Intron 10 of 13
ENSG00000258526	ENST00000652126.1	n.457+16402T>C		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84114 AN: 151764 Hom.: 25378 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.554 AC: 84133 AN: 151886 Hom.: 25383 Cov.: 32 AF XY: 0.549 AC XY: 40766 AN XY: 74218

African (AFR) AF: 0.332 AC: 13762 AN: 41422

American (AMR) AF: 0.549 AC: 8365 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2247 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1244 AN: 5162

South Asian (SAS) AF: 0.509 AC: 2450 AN: 4810

European-Finnish (FIN) AF: 0.640 AC: 6761 AN: 10556

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47266 AN: 67910

Other (OTH) AF: 0.567 AC: 1195 AN: 2106

Alfa AF: 0.656 Hom.: 17163

Bravo AF: 0.537

Asia WGS AF: 0.351 AC: 1219 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.0
DANN	Benign	0.91
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs1950634; hg19: chr14-40141414;