chr14-66313845-C-T

Variant names:

• chr14-66313845-C-T
• rs2053149
• ENST00000556361.1:n.65-64611G>A

Variant summary

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

The ENST00000556361.1(ENSG00000258561):​n.65-64611G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,022 control chromosomes in the GnomAD database, including 7,498 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 0.27 (7498 hom., cov: 32)
• Consequence: ENSG00000258561 ENST00000556361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 3 publications found

Genes affected

ENSG00000258561 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 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
ENSG00000258561	ENST00000556361.1	n.65-64611G>A		intron_variant	Intron 1 of 3	3
ENSG00000258561	ENST00000556874.1	n.644-82950G>A		intron_variant	Intron 4 of 4	2
ENSG00000258561	ENST00000654014.1	n.370-44803G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41401 AN: 151904 Hom.: 7458 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.273 AC: 41505 AN: 152022 Hom.: 7498 Cov.: 32 AF XY: 0.278 AC XY: 20699 AN XY: 74324

African (AFR) AF: 0.469 AC: 19450 AN: 41428

American (AMR) AF: 0.362 AC: 5531 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2473 AN: 5170

South Asian (SAS) AF: 0.318 AC: 1531 AN: 4814

European-Finnish (FIN) AF: 0.150 AC: 1589 AN: 10584

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9278 AN: 67972

Other (OTH) AF: 0.279 AC: 589 AN: 2112

Alfa AF: 0.194 Hom.: 10430

Bravo AF: 0.298

Asia WGS AF: 0.401 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.55
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2053149; hg19: chr14-66780563;