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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377885	XR_001744250.1	n.321+38986G>A		intron_variant	Intron 2 of 4
LOC105377885	XR_001744251.1	n.321+38986G>A		intron_variant	Intron 2 of 3
LOC105377885	XR_001744252.3	n.321+38986G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234426	ENST00000429137.1	n.90+17846G>A		intron_variant	Intron 1 of 2	3
ENSG00000234426	ENST00000648572.1	n.27+17846G>A		intron_variant	Intron 1 of 6
ENSG00000234426	ENST00000655924.1	n.330+38986G>A		intron_variant	Intron 2 of 4

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 v4.3

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;