chr11-32021826-C-T

Variant names:

• chr11-32021826-C-T
• rs10767911
• ENST00000532942.5:c.102-75318C>T

Variant summary

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

The ENST00000532942.5(ENSG00000285283):​c.102-75318C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,572 control chromosomes in the GnomAD database, including 30,763 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 0.62 (30763 hom., cov: 29)
• Consequence: ENSG00000285283 ENST00000532942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 3 publications found

Genes affected

ENSG00000285283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532942.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285283	ENST00000532942.5	TSL:2	c.102-75318C>T		intron	N/A	ENSP00000436422.1
	ENSG00000285283	ENST00000530348.5	TSL:4	c.-244-75318C>T		intron	N/A	ENSP00000436482.1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93777 AN: 151460 Hom.: 30702 Cov.: 29

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.620 AC: 93901 AN: 151572 Hom.: 30763 Cov.: 29 AF XY: 0.620 AC XY: 45895 AN XY: 74064

African (AFR) AF: 0.796 AC: 32909 AN: 41350

American (AMR) AF: 0.668 AC: 10157 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1789 AN: 3466

East Asian (EAS) AF: 0.936 AC: 4818 AN: 5146

South Asian (SAS) AF: 0.625 AC: 2992 AN: 4788

European-Finnish (FIN) AF: 0.443 AC: 4612 AN: 10418

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34571 AN: 67878

Other (OTH) AF: 0.604 AC: 1273 AN: 2106

Alfa AF: 0.566 Hom.: 9789

Bravo AF: 0.648

Asia WGS AF: 0.779 AC: 2705 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.73
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10767911; hg19: chr11-32043372;