chr13-114275713-C-A

Variant names:

• chr13-114275713-C-A
• rs7998576
• ENST00000649577.1:n.815G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649577.1(ENSG00000285672):​n.815G>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 0.311 in 152,014 control chromosomes in the GnomAD database, including 8,587 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 0.31 (8587 hom., cov: 32)
• Consequence: ENSG00000285672 ENST00000649577.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 8 publications found

Genes affected

ENSG00000285672 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649577.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285672	ENST00000649577.1		n.815G>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000289904	ENST00000809305.1		n.449-3791G>T		intron	N/A
	ENSG00000289904	ENST00000809306.1		n.362-2309G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47161 AN: 151896 Hom.: 8573 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.0828

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.302

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.311 AC: 47215 AN: 152014 Hom.: 8587 Cov.: 32 AF XY: 0.310 AC XY: 23019 AN XY: 74322

African (AFR) AF: 0.506 AC: 20952 AN: 41412

American (AMR) AF: 0.293 AC: 4481 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3472

East Asian (EAS) AF: 0.168 AC: 870 AN: 5180

South Asian (SAS) AF: 0.308 AC: 1483 AN: 4820

European-Finnish (FIN) AF: 0.225 AC: 2378 AN: 10568

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15411 AN: 67978

Other (OTH) AF: 0.301 AC: 636 AN: 2112

Alfa AF: 0.289 Hom.: 952

Bravo AF: 0.320

Asia WGS AF: 0.260 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.40
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs7998576; hg19: chr13-115041188;