rs9494142

Variant names:

• chr6-135110502-T-C
• rs9494142
• ENST00000844074.1:n.*42T>C

Variant summary

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

The ENST00000844074.1(ENSG00000309813):​n.*42T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,108 control chromosomes in the GnomAD database, including 3,708 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 0.21 (3708 hom., cov: 32)
• Consequence: ENSG00000309813 ENST00000844074.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64
• Publications: 37 publications found

Genes affected

ENSG00000309813 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378010	XR_001743891.1	n.*85T>C		downstream_gene_variant
LOC105378010	XR_943010.2	n.*85T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309813	ENST00000844074.1	n.*42T>C		downstream_gene_variant
ENSG00000309813	ENST00000844075.1	n.*42T>C		downstream_gene_variant
ENSG00000309813	ENST00000844076.1	n.*46T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31884 AN: 151990 Hom.: 3701 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.210 AC: 31912 AN: 152108 Hom.: 3708 Cov.: 32 AF XY: 0.209 AC XY: 15538 AN XY: 74346

African (AFR) AF: 0.135 AC: 5612 AN: 41512

American (AMR) AF: 0.194 AC: 2972 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3464

East Asian (EAS) AF: 0.274 AC: 1416 AN: 5176

South Asian (SAS) AF: 0.104 AC: 500 AN: 4822

European-Finnish (FIN) AF: 0.326 AC: 3441 AN: 10566

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16671 AN: 67970

Other (OTH) AF: 0.182 AC: 385 AN: 2110

Alfa AF: 0.234 Hom.: 6264

Bravo AF: 0.201

Asia WGS AF: 0.166 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs9494142; hg19: chr6-135431640; COSMIC: COSV60283450;