rs10513402

chr9-122402657-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439471.2(ENSG00000233616):n.37+213A>G variant causes a intron, non coding transcript 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: ENST00000439471.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124902264	XR_007061758.1	n.112+527A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000439471.2	n.37+213A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0887

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0824

Gnomad4 FIN AF: 0.0927

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.112

Alfa AF: 0.114 Hom.: 1363

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513402; hg19: chr9-125164936;