rs11119132

Variant names:

• chr1-208819087-C-A
• rs11119132
• ENST00000718977.1:n.315+2532G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-208819087-C-A
• chr1-208819087-C-T

Variant summary

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

The ENST00000718977.1(ENSG00000293786):​n.315+2532G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 152,212 control chromosomes in the GnomAD database, including 286 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 0.049 (286 hom., cov: 32)
• Consequence: ENSG00000293786 ENST00000718977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 2 publications found

Genes affected

ENSG00000293786 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0729 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718977.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293786	ENST00000718977.1		n.315+2532G>T		intron	N/A
	ENSG00000293786	ENST00000718978.1		n.159-303G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0493 AC: 7494 AN: 152094 Hom.: 287 Cov.: 32

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0492 AC: 7494 AN: 152212 Hom.: 286 Cov.: 32 AF XY: 0.0474 AC XY: 3526 AN XY: 74426

African (AFR) AF: 0.0153 AC: 636 AN: 41548

American (AMR) AF: 0.0376 AC: 575 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0208 AC: 72 AN: 3468

East Asian (EAS) AF: 0.0494 AC: 255 AN: 5166

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4824

European-Finnish (FIN) AF: 0.0535 AC: 566 AN: 10578

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0747 AC: 5078 AN: 68020

Other (OTH) AF: 0.0421 AC: 89 AN: 2112

Alfa AF: 0.0324 Hom.: 33

Bravo AF: 0.0477

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.59
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs11119132; hg19: chr1-208992432;