14-52821964-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000285664 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649005.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285664	ENST00000649005.1		n.417-10273T>C		intron	N/A
	ENSG00000285664	ENST00000653549.1		n.409+29638T>C		intron	N/A
	ENSG00000285664	ENST00000654071.1		n.571+29638T>C		intron	N/A

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

African (AFR) AF: 0.210 AC: 8735 AN: 41550

American (AMR) AF: 0.402 AC: 6140 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2572 AN: 5180

South Asian (SAS) AF: 0.464 AC: 2240 AN: 4828

European-Finnish (FIN) AF: 0.467 AC: 4939 AN: 10576

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27749 AN: 67992

Other (OTH) AF: 0.353 AC: 744 AN: 2110

Alfa AF: 0.389 Hom.: 7049

Bravo AF: 0.348

Asia WGS AF: 0.501 AC: 1739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.68
PhyloP100		0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17125761;

hg19: chr14-53288682;