chr10-100337938-T-C

Variant names:

• chr10-100337938-T-C
• rs2060792
• ENST00000429420.1:n.212-900A>G

Variant summary

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

The ENST00000429420.1(ENSG00000231188):​n.212-900A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,342 control chromosomes in the GnomAD database, including 5,746 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 0.25 (5746 hom., cov: 30)
• Consequence: ENSG00000231188 ENST00000429420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525
• Publications: 16 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429420.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231188	ENST00000429420.1	TSL:3	n.212-900A>G		intron	N/A
	ENSG00000231188	ENST00000775829.1		n.129-900A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37801 AN: 151262 Hom.: 5735 Cov.: 30

Gnomad AFR AF: 0.0734

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.250 AC: 37827 AN: 151342 Hom.: 5746 Cov.: 30 AF XY: 0.247 AC XY: 18256 AN XY: 73860

African (AFR) AF: 0.0732 AC: 3020 AN: 41258

American (AMR) AF: 0.382 AC: 5810 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1048 AN: 3466

East Asian (EAS) AF: 0.344 AC: 1763 AN: 5130

South Asian (SAS) AF: 0.175 AC: 840 AN: 4796

European-Finnish (FIN) AF: 0.253 AC: 2617 AN: 10330

Middle Eastern (MID) AF: 0.286 AC: 83 AN: 290

European-Non Finnish (NFE) AF: 0.321 AC: 21770 AN: 67866

Other (OTH) AF: 0.274 AC: 575 AN: 2098

Alfa AF: 0.289 Hom.: 12478

Bravo AF: 0.258

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.7
DANN	Benign	0.27
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2060792; hg19: chr10-102097695;