rs11504159

Variant names:

• chr12-63681245-T-C
• rs11504159
• ENST00000509615.2:n.239-57421A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-63681245-T-C
• chr12-63681245-T-G

Variant summary

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

The ENST00000509615.2(ENSG00000249753):​n.239-57421A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,694 control chromosomes in the GnomAD database, including 10,299 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 0.37 (10299 hom., cov: 30)
• Consequence: ENSG00000249753 ENST00000509615.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 3 publications found

Genes affected

ENSG00000249753 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509615.2. 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
	ENSG00000249753	ENST00000509615.2	TSL:5	n.239-57421A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55644 AN: 151576 Hom.: 10273 Cov.: 30

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.367 AC: 55718 AN: 151694 Hom.: 10299 Cov.: 30 AF XY: 0.363 AC XY: 26876 AN XY: 74122

African (AFR) AF: 0.406 AC: 16804 AN: 41342

American (AMR) AF: 0.413 AC: 6300 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1492 AN: 3468

East Asian (EAS) AF: 0.269 AC: 1385 AN: 5144

South Asian (SAS) AF: 0.225 AC: 1077 AN: 4790

European-Finnish (FIN) AF: 0.293 AC: 3090 AN: 10536

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.359 AC: 24370 AN: 67860

Other (OTH) AF: 0.371 AC: 777 AN: 2092

Alfa AF: 0.354 Hom.: 1224

Bravo AF: 0.379

Asia WGS AF: 0.259 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.84
PhyloP100		-0.15

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: rs11504159;

hg19: chr12-64075025;