rs11067763

Variant names:

• chr12-115760536-A-G
• rs11067763
• ENST00000549163.1:n.130-4918A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-115760536-A-G
• chr12-115760536-A-T

Variant summary

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

The ENST00000549163.1(ENSG00000257781):​n.130-4918A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,154 control chromosomes in the GnomAD database, including 2,840 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 0.17 (2840 hom., cov: 32)
• Consequence: ENSG00000257781 ENST00000549163.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 18 publications found

Genes affected

ENSG00000257781 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549163.1. 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
	ENSG00000257781	ENST00000549163.1	TSL:3	n.130-4918A>G		intron	N/A
	ENSG00000257781	ENST00000825498.1		n.364-9149A>G		intron	N/A
	ENSG00000257781	ENST00000825499.1		n.192+5146A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25638 AN: 152036 Hom.: 2827 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.169 AC: 25678 AN: 152154 Hom.: 2840 Cov.: 32 AF XY: 0.172 AC XY: 12761 AN XY: 74396

African (AFR) AF: 0.250 AC: 10363 AN: 41448

American (AMR) AF: 0.184 AC: 2812 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2019 AN: 5176

South Asian (SAS) AF: 0.368 AC: 1772 AN: 4818

European-Finnish (FIN) AF: 0.0760 AC: 807 AN: 10616

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6948 AN: 68020

Other (OTH) AF: 0.187 AC: 395 AN: 2114

Alfa AF: 0.129 Hom.: 2177

Bravo AF: 0.179

Asia WGS AF: 0.368 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		-0.020
Mutation Taster		=100/0	polymorphism

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: rs11067763;

hg19: chr12-116198341;