10-106293607-C-T

Variant names:

• chr10-106293607-C-T
• rs7894703
• ENST00000746196.1:n.300+43153G>A

Variant summary

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

The ENST00000746196.1(ENSG00000297210):​n.300+43153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,140 control chromosomes in the GnomAD database, including 44,431 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 0.76 (44431 hom., cov: 33)
• Consequence: ENSG00000297210 ENST00000746196.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.755
• Publications: 2 publications found

Genes affected

ENSG00000297210 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746196.1. 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
	ENSG00000297210	ENST00000746196.1		n.300+43153G>A		intron	N/A
	ENSG00000297231	ENST00000746356.1		n.150+8008C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115860 AN: 152022 Hom.: 44385 Cov.: 33

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.762 AC: 115961 AN: 152140 Hom.: 44431 Cov.: 33 AF XY: 0.762 AC XY: 56653 AN XY: 74364

African (AFR) AF: 0.704 AC: 29210 AN: 41472

American (AMR) AF: 0.803 AC: 12286 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2474 AN: 3472

East Asian (EAS) AF: 0.692 AC: 3574 AN: 5166

South Asian (SAS) AF: 0.715 AC: 3447 AN: 4818

European-Finnish (FIN) AF: 0.803 AC: 8493 AN: 10580

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 54001 AN: 68016

Other (OTH) AF: 0.744 AC: 1572 AN: 2112

Alfa AF: 0.771 Hom.: 30511

Bravo AF: 0.761

Asia WGS AF: 0.696 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.62
PhyloP100		0.76

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: rs7894703;

hg19: chr10-108053365;