rs11169544

Variant names:

• chr12-50750966-T-C
• rs11169544
• ENST00000750012.1:n.239-5991A>G

Variant summary

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

The ENST00000750012.1(ENSG00000297678):​n.239-5991A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,928 control chromosomes in the GnomAD database, including 4,997 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 0.24 (4997 hom., cov: 31)
• Consequence: ENSG00000297678 ENST00000750012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 6 publications found

Genes affected

ENSG00000297678 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902932	XR_007063306.1	n.350-5991A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297678	ENST00000750012.1	n.239-5991A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35728 AN: 151810 Hom.: 4987 Cov.: 31

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.235 AC: 35748 AN: 151928 Hom.: 4997 Cov.: 31 AF XY: 0.245 AC XY: 18220 AN XY: 74232

African (AFR) AF: 0.0866 AC: 3587 AN: 41442

American (AMR) AF: 0.292 AC: 4461 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3468

East Asian (EAS) AF: 0.403 AC: 2077 AN: 5160

South Asian (SAS) AF: 0.334 AC: 1611 AN: 4820

European-Finnish (FIN) AF: 0.365 AC: 3840 AN: 10526

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18185 AN: 67926

Other (OTH) AF: 0.231 AC: 485 AN: 2104

Alfa AF: 0.262 Hom.: 921

Bravo AF: 0.222

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	9.4
DANN	Benign	0.88
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs11169544; hg19: chr12-51144749;