11-121908759-T-C

Variant names:

• chr11-121908759-T-C
• rs1078402
• ENST00000652518.1:n.1724+375T>C

Variant summary

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

The ENST00000652518.1(ENSG00000286044):​n.1724+375T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,954 control chromosomes in the GnomAD database, including 26,112 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 0.57 (26112 hom., cov: 31)
• Consequence: ENSG00000286044 ENST00000652518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.958
• Publications: 3 publications found

Genes affected

ENSG00000286044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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
ENSG00000286044	ENST00000652518.1	n.1724+375T>C		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86782 AN: 151834 Hom.: 26108 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.571 AC: 86802 AN: 151954 Hom.: 26112 Cov.: 31 AF XY: 0.574 AC XY: 42640 AN XY: 74262

African (AFR) AF: 0.368 AC: 15255 AN: 41440

American (AMR) AF: 0.612 AC: 9349 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1967 AN: 3468

East Asian (EAS) AF: 0.779 AC: 4017 AN: 5156

South Asian (SAS) AF: 0.708 AC: 3408 AN: 4816

European-Finnish (FIN) AF: 0.692 AC: 7293 AN: 10536

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43512 AN: 67952

Other (OTH) AF: 0.575 AC: 1209 AN: 2104

Alfa AF: 0.612 Hom.: 101334

Bravo AF: 0.557

Asia WGS AF: 0.745 AC: 2588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	18
DANN	Benign	0.78
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs1078402; hg19: chr11-121779467;