rs10510089

Variant names:

• chr10-121148705-T-C
• rs10510089
• ENST00000741064.1:n.94-29356A>G

Variant summary

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

The ENST00000741064.1(ENSG00000296663):​n.94-29356A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0593 in 152,190 control chromosomes in the GnomAD database, including 546 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 0.059 (546 hom., cov: 32)
• Consequence: ENSG00000296663 ENST00000741064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 0 publications found

Genes affected

ENSG00000296663 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741064.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296663	ENST00000741064.1		n.94-29356A>G		intron	N/A
	ENSG00000296663	ENST00000741065.1		n.85-29356A>G		intron	N/A
	ENSG00000296663	ENST00000741066.1		n.237+18941A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0592 AC: 9007 AN: 152072 Hom.: 542 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0637

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.0247

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0593 AC: 9027 AN: 152190 Hom.: 546 Cov.: 32 AF XY: 0.0606 AC XY: 4514 AN XY: 74430

African (AFR) AF: 0.137 AC: 5673 AN: 41534

American (AMR) AF: 0.0643 AC: 982 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00432 AC: 15 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1083 AN: 5168

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4824

European-Finnish (FIN) AF: 0.0247 AC: 262 AN: 10592

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0114 AC: 778 AN: 67998

Other (OTH) AF: 0.0501 AC: 106 AN: 2114

Alfa AF: 0.0483 Hom.: 62

Bravo AF: 0.0680

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.039
DANN	Benign	0.70
PhyloP100		-2.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10510089;

hg19: chr10-122908219;