chr10-100346610-T-C

Variant names:

• chr10-100346610-T-C
• rs670213
• ENST00000429420.1:n.-220A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429420.1(ENSG00000231188):​n.-220A>G variant causes a upstream gene 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 ENST00000429420.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

ENSG00000231188 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	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

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.566

Alfa AF: 0.509 Hom.: 14833

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs670213; hg19: chr10-102106367;