14-35363460-T-G

Position:

• chr14-35363460-T-G

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

Genes affected

(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/exons	MANE	Protein	UniProt
		n.35363460T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258860	ENST00000555024.1	n.61+108A>C		intron_variant		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;