ENST00000452651.1:n.115-2412C>T

Variant names:

• chr6-160668785-G-A
• rs1084651
• ENST00000452651.1:n.115-2412C>T

Variant summary

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

The ENST00000452651.1(ENSG00000243831):​n.115-2412C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 150,458 control chromosomes in the GnomAD database, including 4,704 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 0.24 (4704 hom., cov: 30)
• Consequence: ENSG00000243831 ENST00000452651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 45 publications found

Genes affected

ENSG00000243831 (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 (EAS) allele frequency at 95% confidence interval = 0.428 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
ENSG00000243831	ENST00000452651.1	n.115-2412C>T		intron_variant	Intron 1 of 1	6
ENSG00000303834	ENST00000797429.1	n.219-482C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35382 AN: 150372 Hom.: 4698 Cov.: 30

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.0742

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.235 AC: 35406 AN: 150458 Hom.: 4704 Cov.: 30 AF XY: 0.239 AC XY: 17550 AN XY: 73440

African (AFR) AF: 0.305 AC: 12446 AN: 40810

American (AMR) AF: 0.346 AC: 5237 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3462

East Asian (EAS) AF: 0.443 AC: 2216 AN: 5000

South Asian (SAS) AF: 0.306 AC: 1439 AN: 4710

European-Finnish (FIN) AF: 0.182 AC: 1897 AN: 10408

Middle Eastern (MID) AF: 0.0799 AC: 23 AN: 288

European-Non Finnish (NFE) AF: 0.165 AC: 11189 AN: 67656

Other (OTH) AF: 0.211 AC: 443 AN: 2098

Alfa AF: 0.194 Hom.: 13439

Asia WGS AF: 0.371 AC: 1287 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	2.6
DANN	Benign	0.58
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1084651; hg19: chr6-161089817;