rs10452600

Variant names:

• chr6-26192274-C-A
• rs10452600
• ENST00000707189.1:n.999+68103C>A

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+68103C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,070 control chromosomes in the GnomAD database, including 1,906 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 0.15 (1906 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 9 publications found

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000707189.1. 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
	ENSG00000291336	ENST00000707189.1		n.999+68103C>A		intron	N/A
	ENSG00000291338	ENST00000707191.1		n.1000+34153C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23432 AN: 151952 Hom.: 1909 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.154 AC: 23437 AN: 152070 Hom.: 1906 Cov.: 32 AF XY: 0.155 AC XY: 11529 AN XY: 74322

African (AFR) AF: 0.177 AC: 7323 AN: 41474

American (AMR) AF: 0.145 AC: 2220 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3464

East Asian (EAS) AF: 0.109 AC: 565 AN: 5172

South Asian (SAS) AF: 0.224 AC: 1080 AN: 4818

European-Finnish (FIN) AF: 0.159 AC: 1683 AN: 10570

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.142 AC: 9689 AN: 67996

Other (OTH) AF: 0.167 AC: 350 AN: 2102

Alfa AF: 0.149 Hom.: 2221

Bravo AF: 0.152

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.4
DANN	Benign	0.64
PhyloP100		0.53

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: rs10452600;

hg19: chr6-26192502;