14-52821964-T-C

Variant names:

• chr14-52821964-T-C
• rs17125761
• ENST00000649005.1:n.417-10273T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649005.1(ENSG00000285664):​n.417-10273T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,194 control chromosomes in the GnomAD database, including 10,572 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 0.36 (10572 hom., cov: 33)
• Consequence: ENSG00000285664 ENST00000649005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.903

Genes affected

ENSG00000285664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370500	XR_007064167.1	n.539+29638T>C		intron_variant	Intron 1 of 2
LOC105370500	XR_943867.3	n.539+29638T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285664	ENST00000649005.1	n.417-10273T>C		intron_variant	Intron 2 of 5
ENSG00000285664	ENST00000653549.1	n.409+29638T>C		intron_variant	Intron 1 of 2
ENSG00000285664	ENST00000654071.1	n.571+29638T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54522 AN: 152076 Hom.: 10565 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.358 AC: 54554 AN: 152194 Hom.: 10572 Cov.: 33 AF XY: 0.365 AC XY: 27116 AN XY: 74388

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.353

Alfa AF: 0.395 Hom.: 3499

Bravo AF: 0.348

Asia WGS AF: 0.501 AC: 1739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17125761; hg19: chr14-53288682;