rs204247

Variant names:

• chr6-13722291-G-A
• rs204247
• ENST00000756652.1:n.159-3772C>T

Variant summary

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

The ENST00000756652.1(ENSG00000298583):​n.159-3772C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,064 control chromosomes in the GnomAD database, including 26,119 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 0.58 (26119 hom., cov: 33)
• Consequence: ENSG00000298583 ENST00000756652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 76 publications found

Genes affected

ENSG00000298583 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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
ENSG00000298583	ENST00000756652.1	n.159-3772C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88720 AN: 151946 Hom.: 26071 Cov.: 33

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.584 AC: 88829 AN: 152064 Hom.: 26119 Cov.: 33 AF XY: 0.582 AC XY: 43271 AN XY: 74310

African (AFR) AF: 0.663 AC: 27505 AN: 41466

American (AMR) AF: 0.571 AC: 8728 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2023 AN: 3472

East Asian (EAS) AF: 0.411 AC: 2122 AN: 5166

South Asian (SAS) AF: 0.557 AC: 2687 AN: 4822

European-Finnish (FIN) AF: 0.558 AC: 5893 AN: 10568

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38080 AN: 67966

Other (OTH) AF: 0.563 AC: 1189 AN: 2112

Alfa AF: 0.572 Hom.: 54884

Bravo AF: 0.588

Asia WGS AF: 0.525 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0080
DANN	Benign	0.47
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs204247; hg19: chr6-13722523;