6-88403098-C-T

Variant names:

• chr6-88403098-C-T
• rs10485165
• ENST00000429137.1:n.90+17846G>A

Variant summary

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

The ENST00000429137.1(ENSG00000234426):​n.90+17846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,054 control chromosomes in the GnomAD database, including 1,722 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 0.13 (1722 hom., cov: 31)
• Consequence: ENSG00000234426 ENST00000429137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684
• Publications: 18 publications found

Genes affected

ENSG00000234426 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429137.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234426	ENST00000429137.1	TSL:3	n.90+17846G>A		intron	N/A
	ENSG00000234426	ENST00000648572.1		n.27+17846G>A		intron	N/A
	ENSG00000234426	ENST00000655924.1		n.330+38986G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20041 AN: 151936 Hom.: 1717 Cov.: 31

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.132 AC: 20056 AN: 152054 Hom.: 1722 Cov.: 31 AF XY: 0.133 AC XY: 9862 AN XY: 74312

African (AFR) AF: 0.0317 AC: 1315 AN: 41490

American (AMR) AF: 0.222 AC: 3390 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1495 AN: 5152

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4806

European-Finnish (FIN) AF: 0.0815 AC: 863 AN: 10584

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10705 AN: 67974

Other (OTH) AF: 0.173 AC: 364 AN: 2110

Alfa AF: 0.152 Hom.: 6626

Bravo AF: 0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.3
DANN	Benign	0.63
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs10485165; hg19: chr6-89112817;