ENST00000653403.1:n.394-1751C>T

Variant names:

• chr11-130774854-G-A
• rs7115849
• ENST00000653403.1:n.394-1751C>T

Variant summary

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

The ENST00000653403.1(ENSG00000288013):​n.394-1751C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,078 control chromosomes in the GnomAD database, including 5,863 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 0.20 (5863 hom., cov: 32)
• Consequence: ENSG00000288013 ENST00000653403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 6 publications found

Genes affected

ENSG00000288013 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369576	XR_001748458.2	n.4413-1751C>T		intron_variant	Intron 3 of 3
LOC105369576	XR_007062955.1	n.7858-1751C>T		intron_variant	Intron 2 of 2
LOC105369576	XR_948197.4	n.445-1751C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288013	ENST00000653403.1	n.394-1751C>T		intron_variant	Intron 2 of 2
ENSG00000288013	ENST00000702122.1	n.456-1751C>T		intron_variant	Intron 3 of 3
ENSG00000288013	ENST00000796886.1	n.281-1751C>T		intron_variant	Intron 1 of 1
ENSG00000288013	ENST00000796887.1	n.521-1751C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30065 AN: 151960 Hom.: 5835 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0236

Gnomad SAS AF: 0.0948

Gnomad FIN AF: 0.0340

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.198 AC: 30142 AN: 152078 Hom.: 5863 Cov.: 32 AF XY: 0.191 AC XY: 14231 AN XY: 74366

African (AFR) AF: 0.507 AC: 20986 AN: 41420

American (AMR) AF: 0.121 AC: 1849 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3470

East Asian (EAS) AF: 0.0234 AC: 121 AN: 5164

South Asian (SAS) AF: 0.0949 AC: 457 AN: 4818

European-Finnish (FIN) AF: 0.0340 AC: 361 AN: 10614

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0748 AC: 5083 AN: 67992

Other (OTH) AF: 0.176 AC: 372 AN: 2108

Alfa AF: 0.131 Hom.: 528

Bravo AF: 0.219

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.43
DANN	Benign	0.68
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs7115849; hg19: chr11-130644749;