6-26436464-C-T

Variant names:

• chr6-26436464-C-T
• rs10456330
• ENST00000707189.1:n.1000-116723C>T

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-116723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0735 in 152,142 control chromosomes in the GnomAD database, including 647 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 0.074 (647 hom., cov: 31)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 6 publications found

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.094 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
ENSG00000291336	ENST00000707189.1	n.1000-116723C>T		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-96241C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0736 AC: 11196 AN: 152022 Hom.: 648 Cov.: 31

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0606

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0960

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0735 AC: 11187 AN: 152142 Hom.: 647 Cov.: 31 AF XY: 0.0775 AC XY: 5761 AN XY: 74378

African (AFR) AF: 0.0162 AC: 673 AN: 41516

American (AMR) AF: 0.0603 AC: 923 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.0744 AC: 386 AN: 5190

South Asian (SAS) AF: 0.0218 AC: 105 AN: 4822

European-Finnish (FIN) AF: 0.215 AC: 2273 AN: 10556

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0960 AC: 6523 AN: 67974

Other (OTH) AF: 0.0525 AC: 111 AN: 2114

Alfa AF: 0.0626 Hom.: 96

Bravo AF: 0.0605

Asia WGS AF: 0.0310 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.67
DANN	Benign	0.40
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10456330; hg19: chr6-26436692;