11-115612450-T-C

Variant names:

• chr11-115612450-T-C
• rs2846903
• ENST00000807517.1:n.441-9805T>C

Variant summary

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

The ENST00000807517.1(ENSG00000255689):​n.441-9805T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,010 control chromosomes in the GnomAD database, including 37,500 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 0.70 (37500 hom., cov: 31)
• Consequence: ENSG00000255689 ENST00000807517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 2 publications found

Genes affected

ENSG00000255689 (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 = 0.748 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
ENSG00000255689	ENST00000807517.1	n.441-9805T>C		intron_variant	Intron 3 of 3
ENSG00000255689	ENST00000807524.1	n.266-9805T>C		intron_variant	Intron 2 of 2
ENSG00000255689	ENST00000807605.1	n.205-11456T>C		intron_variant	Intron 1 of 3
ENSG00000255689	ENST00000807606.1	n.232-16120T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106329 AN: 151892 Hom.: 37442 Cov.: 31

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.700 AC: 106451 AN: 152010 Hom.: 37500 Cov.: 31 AF XY: 0.697 AC XY: 51791 AN XY: 74284

African (AFR) AF: 0.755 AC: 31309 AN: 41468

American (AMR) AF: 0.671 AC: 10250 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2274 AN: 3470

East Asian (EAS) AF: 0.509 AC: 2620 AN: 5152

South Asian (SAS) AF: 0.660 AC: 3170 AN: 4806

European-Finnish (FIN) AF: 0.689 AC: 7272 AN: 10560

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47331 AN: 67962

Other (OTH) AF: 0.676 AC: 1428 AN: 2112

Alfa AF: 0.711 Hom.: 9194

Bravo AF: 0.700

Asia WGS AF: 0.581 AC: 2023 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	0.14
DANN	Benign	0.20
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2846903; hg19: chr11-115483168;