chr10-100346610-T-C

Variant names:

• chr10-100346610-T-C
• rs670213
• ENST00000746873.1:n.388A>G

Variant summary

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

The ENST00000746873.1(ENSG00000231188):​n.388A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,992 control chromosomes in the GnomAD database, including 29,885 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 0.61 (29885 hom., cov: 33)
• Consequence: ENSG00000231188 ENST00000746873.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 14 publications found

Genes affected

ENSG00000231188 (HGNC:58401):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231188	ENST00000746873.1	n.388A>G		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000231188	ENST00000429420.1	n.-220A>G		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92782 AN: 151874 Hom.: 29843 Cov.: 33

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.611 AC: 92873 AN: 151992 Hom.: 29885 Cov.: 33 AF XY: 0.617 AC XY: 45825 AN XY: 74292

African (AFR) AF: 0.825 AC: 34255 AN: 41508

American (AMR) AF: 0.493 AC: 7529 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3470

East Asian (EAS) AF: 0.656 AC: 3371 AN: 5142

South Asian (SAS) AF: 0.681 AC: 3287 AN: 4824

European-Finnish (FIN) AF: 0.614 AC: 6485 AN: 10562

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34430 AN: 67890

Other (OTH) AF: 0.566 AC: 1195 AN: 2110

Alfa AF: 0.516 Hom.: 17802

Bravo AF: 0.605

Asia WGS AF: 0.681 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.41
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs670213; hg19: chr10-102106367;