ENST00000775477.1:n.108+35A>C

Variant names:

• chr1-8257898-A-C
• rs7520292
• ENST00000775477.1:n.108+35A>C

Variant summary

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

The ENST00000775477.1(ENSG00000301006):​n.108+35A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 151,400 control chromosomes in the GnomAD database, including 45,615 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 0.77 (45615 hom., cov: 27)
• Consequence: ENSG00000301006 ENST00000775477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 publications found

Genes affected

ENSG00000301006 (HGNC:58485):

ENSG00000301025 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 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
ENSG00000301006	ENST00000775477.1	n.108+35A>C		intron_variant	Intron 1 of 1
ENSG00000301006	ENST00000775483.1	n.88+454A>C		intron_variant	Intron 1 of 2
ENSG00000301025	ENST00000775652.1	n.278-1295T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117061 AN: 151282 Hom.: 45596 Cov.: 27

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.774 AC: 117139 AN: 151400 Hom.: 45615 Cov.: 27 AF XY: 0.769 AC XY: 56832 AN XY: 73920

African (AFR) AF: 0.779 AC: 32153 AN: 41260

American (AMR) AF: 0.694 AC: 10513 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2514 AN: 3466

East Asian (EAS) AF: 0.605 AC: 3072 AN: 5076

South Asian (SAS) AF: 0.624 AC: 2976 AN: 4770

European-Finnish (FIN) AF: 0.836 AC: 8760 AN: 10476

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.804 AC: 54587 AN: 67898

Other (OTH) AF: 0.755 AC: 1585 AN: 2100

Alfa AF: 0.783 Hom.: 7899

Bravo AF: 0.768

Asia WGS AF: 0.637 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.53
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7520292; hg19: chr1-8317958;