chr6-135262485-A-C

Variant names:

• chr6-135262485-A-C
• rs9494193
• ENST00000791085.1:n.*164A>C

Variant summary

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

The ENST00000791085.1(ENSG00000224374):​n.*164A>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,076 control chromosomes in the GnomAD database, including 18,947 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 0.46 (18947 hom., cov: 32)
• Consequence: ENSG00000224374 ENST00000791085.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

Genes affected

ENSG00000224374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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
ENSG00000224374	ENST00000791085.1	n.*164A>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70248 AN: 151956 Hom.: 18911 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.463 AC: 70348 AN: 152076 Hom.: 18947 Cov.: 32 AF XY: 0.459 AC XY: 34153 AN XY: 74330

African (AFR) AF: 0.753 AC: 31229 AN: 41494

American (AMR) AF: 0.331 AC: 5062 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1763 AN: 5166

South Asian (SAS) AF: 0.415 AC: 2001 AN: 4820

European-Finnish (FIN) AF: 0.337 AC: 3566 AN: 10572

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24389 AN: 67954

Other (OTH) AF: 0.423 AC: 892 AN: 2108

Alfa AF: 0.368 Hom.: 4316

Bravo AF: 0.470

Asia WGS AF: 0.412 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.041
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9494193; hg19: chr6-135583623;