13-99406307-G-A

Position:

• chr13-99406307-G-A

Variant summary

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

The ENST00000642991.1(ENSG00000290577):​n.2921C>T 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 0.713 in 152,158 control chromosomes in the GnomAD database, including 39,548 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 0.71 (39537 hom., cov: 32)
  • Exomes 𝑓: 0.84 (11 hom.)
• Consequence: ENSG00000290577 ENST00000642991.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

Genes affected

ENSG00000290577 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.99406307G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290577	ENST00000642991.1	n.2921C>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108431 AN: 152008 Hom.: 39524 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.708

GnomAD4 exome AF: 0.844 AC: 27 AN: 32 Hom.: 11 Cov.: 0 AF XY: 0.833 AC XY: 20 AN XY: 24

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.857

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.713 AC: 108481 AN: 152126 Hom.: 39537 Cov.: 32 AF XY: 0.711 AC XY: 52910 AN XY: 74392

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.707

Alfa AF: 0.786 Hom.: 87635

Bravo AF: 0.703

Asia WGS AF: 0.627 AC: 2183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2892976; hg19: chr13-100058561;