rs710285

Positions:

• chr14-98068349-A-G

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.433T>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 0.413 in 152,032 control chromosomes in the GnomAD database, including 13,116 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 0.41 (13113 hom., cov: 32)
  • Exomes 𝑓: 0.57 (3 hom.)
• Consequence: ENST00000555776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.46

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370655	XR_001750876.2	n.9580T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000555776.1	n.433T>C		non_coding_transcript_exon_variant	3/3	4
	ENST00000663808.1	n.516T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62794 AN: 151900 Hom.: 13099 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.571 AC: 8 AN: 14 Hom.: 3 Cov.: 0 AF XY: 0.700 AC XY: 7 AN XY: 10

Gnomad4 NFE exome AF: 0.583

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.413 AC: 62850 AN: 152018 Hom.: 13113 Cov.: 32 AF XY: 0.412 AC XY: 30594 AN XY: 74318

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.439

Alfa AF: 0.421 Hom.: 6939

Bravo AF: 0.419

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.030
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs710285; hg19: chr14-98534686;