rs7998576

Positions:

• chr13-114275713-C-A

Variant summary

Our verdict is Benign. Variant got -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: ENST00000649577.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370384	XR_007063887.1	n.968-3791G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649577.1	n.815G>T		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.301

Alfa AF: 0.279 Hom.: 842

Bravo AF: 0.320

Asia WGS AF: 0.260 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7998576; hg19: chr13-115041188;