14-24634456-T-C

Position:

• chr14-24634456-T-C

Variant summary

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

The ENST00000557736.5(ENSG00000258657):​n.600T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 444,166 control chromosomes in the GnomAD database, including 71,132 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 0.53 (21534 hom., cov: 32)
  • Exomes 𝑓: 0.58 (49598 hom.)
• Consequence: ENSG00000258657 ENST00000557736.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531

Genes affected

ENSG00000258657 (HGNC:58166):

LOC105370413 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370413	XR_007064087.1	n.408T>C		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258657	ENST00000557736.5	n.600T>C		non_coding_transcript_exon_variant	3/3	4
ENSG00000258657	ENST00000555300.1	n.177+11330T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79760 AN: 151838 Hom.: 21526 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.514

GnomAD4 exome AF: 0.577 AC: 168464 AN: 292208 Hom.: 49598 Cov.: 4 AF XY: 0.583 AC XY: 90848 AN XY: 155732

Gnomad4 AFR exome AF: 0.440

Gnomad4 AMR exome AF: 0.332

Gnomad4 ASJ exome AF: 0.606

Gnomad4 EAS exome AF: 0.457

Gnomad4 SAS exome AF: 0.615

Gnomad4 FIN exome AF: 0.554

Gnomad4 NFE exome AF: 0.606

Gnomad4 OTH exome AF: 0.568

GnomAD4 genome AF: 0.525 AC: 79804 AN: 151958 Hom.: 21534 Cov.: 32 AF XY: 0.521 AC XY: 38668 AN XY: 74282

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.515

Alfa AF: 0.588 Hom.: 57626

Bravo AF: 0.504

Asia WGS AF: 0.490 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7144366; hg19: chr14-25103662; COSMIC: COSV53543675;