11-81260098-A-G

Variant names:

• chr11-81260098-A-G
• rs936368
• ENST00000671134.1:n.324-14778A>G

Variant summary

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

The ENST00000671134.1(ENSG00000287912):​n.324-14778A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 151,646 control chromosomes in the GnomAD database, including 54,082 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 0.84 (54082 hom., cov: 33)
• Consequence: ENSG00000287912 ENST00000671134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 4 publications found

Genes affected

ENSG00000287912 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671134.1. 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
	ENSG00000287912	ENST00000671134.1		n.324-14778A>G		intron	N/A
	ENSG00000287912	ENST00000671210.1		n.310-14778A>G		intron	N/A
	ENSG00000287912	ENST00000701193.2		n.196-14778A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.844 AC: 127936 AN: 151528 Hom.: 54045 Cov.: 33

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.844 AC: 128026 AN: 151646 Hom.: 54082 Cov.: 33 AF XY: 0.847 AC XY: 62767 AN XY: 74130

African (AFR) AF: 0.848 AC: 35128 AN: 41432

American (AMR) AF: 0.855 AC: 12997 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2943 AN: 3462

East Asian (EAS) AF: 0.971 AC: 4972 AN: 5120

South Asian (SAS) AF: 0.878 AC: 4227 AN: 4816

European-Finnish (FIN) AF: 0.842 AC: 8882 AN: 10548

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.828 AC: 56130 AN: 67764

Other (OTH) AF: 0.822 AC: 1725 AN: 2098

Alfa AF: 0.833 Hom.: 179795

Bravo AF: 0.847

Asia WGS AF: 0.910 AC: 3166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.088
DANN	Benign	0.49
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs936368;

hg19: chr11-80971141;