rs6013897

Variant names:

• chr20-54125940-T-A
• rs6013897
• ENST00000792273.1:n.154+15426T>A

Your query was ambiguous. Multiple possible variants found:

• chr20-54125940-T-A
• chr20-54125940-T-C

Variant summary

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

The ENST00000792273.1(ENSG00000286587):​n.154+15426T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,124 control chromosomes in the GnomAD database, including 4,269 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 0.23 (4269 hom., cov: 32)
• Consequence: ENSG00000286587 ENST00000792273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 187 publications found

Genes affected

ENSG00000286587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.312 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
ENSG00000286587	ENST00000792273.1	n.154+15426T>A		intron_variant	Intron 2 of 3
ENSG00000286587	ENST00000792274.1	n.144+15426T>A		intron_variant	Intron 2 of 6
ENSG00000286587	ENST00000792275.1	n.186+15426T>A		intron_variant	Intron 1 of 2
ENSG00000286587	ENST00000792276.1	n.125+2023T>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35370 AN: 152006 Hom.: 4256 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.233 AC: 35430 AN: 152124 Hom.: 4269 Cov.: 32 AF XY: 0.234 AC XY: 17402 AN XY: 74376

African (AFR) AF: 0.245 AC: 10163 AN: 41492

American (AMR) AF: 0.320 AC: 4886 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3470

East Asian (EAS) AF: 0.144 AC: 746 AN: 5178

South Asian (SAS) AF: 0.309 AC: 1491 AN: 4822

European-Finnish (FIN) AF: 0.233 AC: 2460 AN: 10580

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14120 AN: 67992

Other (OTH) AF: 0.239 AC: 505 AN: 2114

Alfa AF: 0.109 Hom.: 164

Bravo AF: 0.240

Asia WGS AF: 0.228 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.65
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6013897; hg19: chr20-52742479;