13-99432425-T-C

Position:

• chr13-99432425-T-C

Variant summary

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

The ENST00000646895.1(ENSG00000285448):​n.278A>G 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 0.654 in 152,160 control chromosomes in the GnomAD database, including 33,588 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 0.65 (33579 hom., cov: 33)
  • Exomes 𝑓: 0.86 (9 hom.)
• Consequence: ENST00000646895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646895.1	n.278A>G		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99405 AN: 152020 Hom.: 33565 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.650

GnomAD4 exome AF: 0.864 AC: 19 AN: 22 Hom.: 9 Cov.: 0 AF XY: 0.917 AC XY: 11 AN XY: 12

Gnomad4 FIN exome AF: 0.800

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.654 AC: 99464 AN: 152138 Hom.: 33579 Cov.: 33 AF XY: 0.654 AC XY: 48647 AN XY: 74364

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.652

Alfa AF: 0.133 Hom.: 72

Bravo AF: 0.647

Asia WGS AF: 0.574 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9517723; hg19: chr13-100084679;