rs10500872

Variant names:

• chr11-20224177-T-C
• rs10500872
• ENST00000725917.1:n.616+272T>C

Variant summary

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

The ENST00000725917.1(ENSG00000294773):​n.616+272T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,156 control chromosomes in the GnomAD database, including 1,625 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 0.14 (1625 hom., cov: 32)
• Consequence: ENSG00000294773 ENST00000725917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• Publications: 3 publications found

Genes affected

ENSG00000294773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 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
ENSG00000294773	ENST00000725917.1	n.616+272T>C		intron_variant	Intron 5 of 5
ENSG00000294773	ENST00000725918.1	n.178+5217T>C		intron_variant	Intron 2 of 2
ENSG00000294773	ENST00000725920.1	n.344+272T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21652 AN: 152038 Hom.: 1622 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0981

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.142 AC: 21654 AN: 152156 Hom.: 1625 Cov.: 32 AF XY: 0.139 AC XY: 10376 AN XY: 74404

African (AFR) AF: 0.123 AC: 5085 AN: 41510

American (AMR) AF: 0.137 AC: 2087 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1064 AN: 5170

South Asian (SAS) AF: 0.166 AC: 800 AN: 4822

European-Finnish (FIN) AF: 0.0981 AC: 1039 AN: 10596

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.154 AC: 10493 AN: 67986

Other (OTH) AF: 0.161 AC: 340 AN: 2110

Alfa AF: 0.156 Hom.: 3734

Bravo AF: 0.145

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.90
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs10500872; hg19: chr11-20245723;