rs11061209

Variant names:

• chr12-130880443-G-A
• rs11061209
• ENST00000728158.1:n.500+765G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-130880443-G-A
• chr12-130880443-G-C
• chr12-130880443-G-T

Variant summary

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

The ENST00000728158.1(ENSG00000295116):​n.500+765G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,988 control chromosomes in the GnomAD database, including 7,254 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 0.30 (7254 hom., cov: 32)
• Consequence: ENSG00000295116 ENST00000728158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 19 publications found

Genes affected

ENSG00000295116 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 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
ENSG00000295116	ENST00000728158.1	n.500+765G>A		intron_variant	Intron 1 of 1
ENSG00000295116	ENST00000728159.1	n.341+765G>A		intron_variant	Intron 1 of 1
ENSG00000295116	ENST00000728160.1	n.316+765G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46260 AN: 151870 Hom.: 7249 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.304 AC: 46276 AN: 151988 Hom.: 7254 Cov.: 32 AF XY: 0.306 AC XY: 22729 AN XY: 74268

African (AFR) AF: 0.239 AC: 9914 AN: 41456

American (AMR) AF: 0.313 AC: 4782 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1146 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1101 AN: 5166

South Asian (SAS) AF: 0.219 AC: 1052 AN: 4812

European-Finnish (FIN) AF: 0.425 AC: 4484 AN: 10556

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22808 AN: 67954

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.320 Hom.: 34124

Bravo AF: 0.293

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs11061209; hg19: chr12-131364988;