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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724439	XR_428810.4	n.132+8008C>T		intron_variant	Intron 1 of 2
LOC102724439	XR_946297.3	n.132+8008C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297210	ENST00000746196.1	n.300+43153G>A		intron_variant	Intron 1 of 1
ENSG00000297231	ENST00000746356.1	n.150+8008C>T		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs7894703; hg19: chr10-108053365;