rs601746

Variant names:

• chr10-95182526-T-C
• rs601746
• ENST00000786483.1:n.691-38108A>G

Variant summary

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

The ENST00000786483.1(ENSG00000234026):​n.691-38108A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,236 control chromosomes in the GnomAD database, including 2,144 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 0.16 (2144 hom., cov: 33)
• Consequence: ENSG00000234026 ENST00000786483.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 5 publications found

Genes affected

ENSG00000234026 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786483.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234026	ENST00000786483.1		n.691-38108A>G		intron	N/A
	ENSG00000234026	ENST00000786484.1		n.562-38108A>G		intron	N/A
	ENSG00000234026	ENST00000786485.1		n.726-38108A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24338 AN: 152118 Hom.: 2143 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.160 AC: 24351 AN: 152236 Hom.: 2144 Cov.: 33 AF XY: 0.158 AC XY: 11797 AN XY: 74436

African (AFR) AF: 0.132 AC: 5476 AN: 41538

American (AMR) AF: 0.181 AC: 2775 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3472

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5194

South Asian (SAS) AF: 0.0805 AC: 389 AN: 4830

European-Finnish (FIN) AF: 0.153 AC: 1624 AN: 10592

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12467 AN: 67994

Other (OTH) AF: 0.200 AC: 422 AN: 2114

Alfa AF: 0.187 Hom.: 2368

Bravo AF: 0.162

Asia WGS AF: 0.0460 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.56
DANN	Benign	0.61
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs601746; hg19: chr10-96942283;