rs10513402

Variant names:

• chr9-122402657-T-C
• rs10513402
• ENST00000439471.3:n.133+213A>G

Variant summary

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

The ENST00000439471.3(ENSG00000233616):​n.133+213A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,134 control chromosomes in the GnomAD database, including 1,042 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 0.11 (1042 hom., cov: 31)
• Consequence: ENSG00000233616 ENST00000439471.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 9 publications found

Genes affected

ENSG00000233616 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902264	XR_007061758.1	n.112+527A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233616	ENST00000439471.3	n.133+213A>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16924 AN: 152016 Hom.: 1030 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.0927

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.112 AC: 16970 AN: 152134 Hom.: 1042 Cov.: 31 AF XY: 0.112 AC XY: 8329 AN XY: 74376

African (AFR) AF: 0.116 AC: 4794 AN: 41494

American (AMR) AF: 0.163 AC: 2488 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0887 AC: 308 AN: 3472

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5180

South Asian (SAS) AF: 0.0824 AC: 397 AN: 4820

European-Finnish (FIN) AF: 0.0927 AC: 982 AN: 10592

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7662 AN: 67984

Other (OTH) AF: 0.112 AC: 235 AN: 2106

Alfa AF: 0.114 Hom.: 1752

Bravo AF: 0.115

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.3
DANN	Benign	0.64
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs10513402; hg19: chr9-125164936;