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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370003	XR_945388.3	n.118+2412T>C		intron_variant	Intron 1 of 3
LOC105370003	XR_945389.3	n.118+2412T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257781	ENST00000549163.1	n.130-4918A>G		intron_variant	Intron 1 of 2	3
ENSG00000257781	ENST00000825498.1	n.364-9149A>G		intron_variant	Intron 1 of 1
ENSG00000257781	ENST00000825499.1	n.192+5146A>G		intron_variant	Intron 1 of 2
ENSG00000257781	ENST00000825500.1	n.254+2100A>G		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs11067763; hg19: chr12-116198341;