11-118847776-C-T

Variant names:

• chr11-118847776-C-T
• rs4938561
• ENST00000816613.1:n.124+19399G>A

Variant summary

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

The ENST00000816613.1(ENSG00000306274):​n.124+19399G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,024 control chromosomes in the GnomAD database, including 48,240 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 0.79 (48240 hom., cov: 30)
• Consequence: ENSG00000306274 ENST00000816613.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 10 publications found

Genes affected

ENSG00000306274 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 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
ENSG00000306274	ENST00000816613.1	n.124+19399G>A		intron_variant	Intron 2 of 2
ENSG00000306274	ENST00000816614.1	n.273-13204G>A		intron_variant	Intron 2 of 2
ENSG00000306274	ENST00000816615.1	n.252-6333G>A		intron_variant	Intron 1 of 1
ENSG00000306274	ENST00000816616.1	n.*223G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120636 AN: 151904 Hom.: 48176 Cov.: 30

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.794 AC: 120759 AN: 152024 Hom.: 48240 Cov.: 30 AF XY: 0.790 AC XY: 58713 AN XY: 74288

African (AFR) AF: 0.877 AC: 36407 AN: 41508

American (AMR) AF: 0.853 AC: 12990 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2823 AN: 3464

East Asian (EAS) AF: 0.726 AC: 3736 AN: 5148

South Asian (SAS) AF: 0.609 AC: 2935 AN: 4816

European-Finnish (FIN) AF: 0.723 AC: 7634 AN: 10560

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51598 AN: 67978

Other (OTH) AF: 0.797 AC: 1684 AN: 2112

Alfa AF: 0.765 Hom.: 74514

Bravo AF: 0.811

Asia WGS AF: 0.685 AC: 2385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs4938561; hg19: chr11-118718485;