1-40926546-C-A

Variant names:

• chr1-40926546-C-A
• rs11591064
• ENST00000775761.1:n.*98G>T

Variant summary

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

The ENST00000775761.1(ENSG00000301041):​n.*98G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,020 control chromosomes in the GnomAD database, including 985 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 0.11 (985 hom., cov: 31)
• Consequence: ENSG00000301041 ENST00000775761.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437
• Publications: 1 publications found

Genes affected

ENSG00000301041 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 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
ENSG00000301041	ENST00000775761.1	n.*98G>T		downstream_gene_variant
ENSG00000301041	ENST00000775762.1	n.*86G>T		downstream_gene_variant
ENSG00000301041	ENST00000775763.1	n.*98G>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16345 AN: 151904 Hom.: 987 Cov.: 31

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.107 AC: 16338 AN: 152020 Hom.: 985 Cov.: 31 AF XY: 0.104 AC XY: 7748 AN XY: 74324

African (AFR) AF: 0.0681 AC: 2825 AN: 41472

American (AMR) AF: 0.107 AC: 1629 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3470

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5176

South Asian (SAS) AF: 0.0927 AC: 446 AN: 4810

European-Finnish (FIN) AF: 0.0925 AC: 979 AN: 10588

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.143 AC: 9727 AN: 67938

Other (OTH) AF: 0.123 AC: 259 AN: 2106

Alfa AF: 0.0543 Hom.: 68

Bravo AF: 0.107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.53
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs11591064; hg19: chr1-41392218; COSMIC: COSV59940700;