rs10500736

Variant names:

• chr11-10985161-T-C
• rs10500736
• ENST00000837199.1:n.296-26761T>C

Variant summary

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

The ENST00000837199.1(ZBED5-AS1):​n.296-26761T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,886 control chromosomes in the GnomAD database, including 8,524 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 0.33 (8524 hom., cov: 31)
• Consequence: ZBED5-AS1 ENST00000837199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 0 publications found

Genes affected

ZBED5-AS1 (HGNC:48646): (ZBED5 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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
ZBED5-AS1	ENST00000837199.1	n.296-26761T>C		intron_variant	Intron 2 of 4
ZBED5-AS1	ENST00000837200.1	n.690+1542T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49713 AN: 151768 Hom.: 8511 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.328 AC: 49759 AN: 151886 Hom.: 8524 Cov.: 31 AF XY: 0.325 AC XY: 24153 AN XY: 74212

African (AFR) AF: 0.427 AC: 17665 AN: 41360

American (AMR) AF: 0.316 AC: 4822 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3472

East Asian (EAS) AF: 0.131 AC: 677 AN: 5176

South Asian (SAS) AF: 0.270 AC: 1303 AN: 4818

European-Finnish (FIN) AF: 0.266 AC: 2805 AN: 10556

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20348 AN: 67924

Other (OTH) AF: 0.320 AC: 675 AN: 2108

Alfa AF: 0.313 Hom.: 2919

Bravo AF: 0.334

Asia WGS AF: 0.229 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.87
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs10500736; hg19: chr11-11006708;