rs8001641

Positions:

• chr13-80118676-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000647704.1(ENSG00000285684):​n.2542C>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 0.364 in 151,996 control chromosomes in the GnomAD database, including 11,862 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 0.36 (11862 hom., cov: 32)
• Consequence: ENST00000647704.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000647704.1	n.2542C>T		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55291 AN: 151878 Hom.: 11864 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.364 AC: 55303 AN: 151996 Hom.: 11862 Cov.: 32 AF XY: 0.360 AC XY: 26730 AN XY: 74272

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.368

Alfa AF: 0.458 Hom.: 17763

Bravo AF: 0.349

Asia WGS AF: 0.190 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	14
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8001641; hg19: chr13-80692811;