14-35363460-T-G

Variant names:

• chr14-35363460-T-G
• rs8016947
• ENST00000555024.1:n.61+108A>C

Variant summary

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

The ENST00000555024.1(ENSG00000258860):​n.61+108A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,102 control chromosomes in the GnomAD database, including 27,302 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 0.60 (27295 hom., cov: 32)
  • Exomes 𝑓: 0.63 (7 hom.)
• Consequence: ENSG00000258860 ENST00000555024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

Genes affected

ENSG00000258860 (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 (AMR) allele frequency at 95% confidence interval = 0.683 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
ENSG00000258860	ENST00000555024.1	n.61+108A>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90675 AN: 151952 Hom.: 27261 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.583

GnomAD4 exome AF: 0.625 AC: 20 AN: 32 Hom.: 7 AF XY: 0.875 AC XY: 14 AN XY: 16

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.650

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.597 AC: 90770 AN: 152070 Hom.: 27295 Cov.: 32 AF XY: 0.597 AC XY: 44388 AN XY: 74330

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.582

Alfa AF: 0.565 Hom.: 51516

Bravo AF: 0.609

Asia WGS AF: 0.601 AC: 2088 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	0.78
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8016947; hg19: chr14-35832666;