11-102486548-C-T

Variant names:

• chr11-102486548-C-T
• rs10750642
• ENST00000529278.2:n.115-7232C>T

Variant summary

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

The ENST00000529278.2(ENSG00000255482):​n.115-7232C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,970 control chromosomes in the GnomAD database, including 28,278 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 0.61 (28278 hom., cov: 32)
• Consequence: ENSG00000255482 ENST00000529278.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 3 publications found

Genes affected

ENSG00000255482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000529278.2. 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
	LOC102723838	NR_135076.1		n.115-7232C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255482	ENST00000529278.2	TSL:2	n.115-7232C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92084 AN: 151854 Hom.: 28255 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.606 AC: 92153 AN: 151970 Hom.: 28278 Cov.: 32 AF XY: 0.602 AC XY: 44749 AN XY: 74282

African (AFR) AF: 0.548 AC: 22692 AN: 41426

American (AMR) AF: 0.639 AC: 9762 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2374 AN: 3466

East Asian (EAS) AF: 0.348 AC: 1794 AN: 5162

South Asian (SAS) AF: 0.544 AC: 2618 AN: 4810

European-Finnish (FIN) AF: 0.551 AC: 5826 AN: 10570

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45078 AN: 67954

Other (OTH) AF: 0.616 AC: 1299 AN: 2110

Alfa AF: 0.647 Hom.: 132958

Bravo AF: 0.611

Asia WGS AF: 0.460 AC: 1601 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.54
DANN	Benign	0.61
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs10750642; hg19: chr11-102357279;