rs1365406

Variant names:

• chr11-12541173-A-G
• rs1365406
• ENST00000526112.1:n.-206T>C

Variant summary

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

The ENST00000526112.1(ENSG00000254847):​n.-206T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,182 control chromosomes in the GnomAD database, including 26,586 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 0.59 (26586 hom., cov: 35)
• Consequence: ENSG00000254847 ENST00000526112.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 5 publications found

Genes affected

ENSG00000254847 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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
ENSG00000254847	ENST00000526112.1	n.-206T>C		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89263 AN: 152064 Hom.: 26557 Cov.: 35

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.587 AC: 89336 AN: 152182 Hom.: 26586 Cov.: 35 AF XY: 0.580 AC XY: 43122 AN XY: 74374

African (AFR) AF: 0.645 AC: 26805 AN: 41530

American (AMR) AF: 0.456 AC: 6967 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3472

East Asian (EAS) AF: 0.513 AC: 2654 AN: 5174

South Asian (SAS) AF: 0.505 AC: 2436 AN: 4820

European-Finnish (FIN) AF: 0.597 AC: 6327 AN: 10594

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40490 AN: 67982

Other (OTH) AF: 0.573 AC: 1211 AN: 2112

Alfa AF: 0.588 Hom.: 102446

Bravo AF: 0.579

Asia WGS AF: 0.497 AC: 1727 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.77
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1365406; hg19: chr11-12562720;