rs8001641

Variant names:

• chr13-80118676-G-A
• rs8001641
• ENST00000647704.1:n.2542C>T

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: ENSG00000285684 ENST00000647704.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

Genes affected

ENSG00000285684 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285684	ENST00000647704.1	n.2542C>T		non_coding_transcript_exon_variant	Exon 3 of 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;