chr11-118161271-G-A

Variant names:

• chr11-118161271-G-A
• rs11600901
• ENST00000845474.1:n.307+3817G>A

Variant summary

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

The ENST00000845474.1(ENSG00000309913):​n.307+3817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0746 in 152,116 control chromosomes in the GnomAD database, including 523 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 0.075 (523 hom., cov: 31)
• Consequence: ENSG00000309913 ENST00000845474.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925
• Publications: 8 publications found

Genes affected

ENSG00000309913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0953 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
ENSG00000309913	ENST00000845474.1	n.307+3817G>A		intron_variant	Intron 2 of 2
ENSG00000309913	ENST00000845475.1	n.142+3817G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0747 AC: 11355 AN: 151998 Hom.: 523 Cov.: 31

Gnomad AFR AF: 0.0269

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0858

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0972

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.0746 AC: 11351 AN: 152116 Hom.: 523 Cov.: 31 AF XY: 0.0759 AC XY: 5644 AN XY: 74356

African (AFR) AF: 0.0268 AC: 1113 AN: 41486

American (AMR) AF: 0.0694 AC: 1061 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3464

East Asian (EAS) AF: 0.0178 AC: 92 AN: 5172

South Asian (SAS) AF: 0.0852 AC: 411 AN: 4822

European-Finnish (FIN) AF: 0.127 AC: 1340 AN: 10582

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.0973 AC: 6613 AN: 67988

Other (OTH) AF: 0.0838 AC: 177 AN: 2112

Alfa AF: 0.0811 Hom.: 838

Bravo AF: 0.0668

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs11600901; hg19: chr11-118031986;