rs766325

Variant names:

• chr1-18629964-G-A
• rs766325
• ENST00000769462.1:n.75+820C>T

Variant summary

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

The ENST00000769462.1(ENSG00000300147):​n.75+820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,096 control chromosomes in the GnomAD database, including 27,281 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 0.58 (27281 hom., cov: 33)
• Consequence: ENSG00000300147 ENST00000769462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 16 publications found

Genes affected

ENSG00000300147 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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
ENSG00000300147	ENST00000769462.1	n.75+820C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88274 AN: 151978 Hom.: 27223 Cov.: 33

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.581 AC: 88396 AN: 152096 Hom.: 27281 Cov.: 33 AF XY: 0.579 AC XY: 43055 AN XY: 74326

African (AFR) AF: 0.780 AC: 32395 AN: 41510

American (AMR) AF: 0.492 AC: 7527 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1833 AN: 3470

East Asian (EAS) AF: 0.172 AC: 889 AN: 5174

South Asian (SAS) AF: 0.452 AC: 2176 AN: 4818

European-Finnish (FIN) AF: 0.602 AC: 6366 AN: 10582

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35571 AN: 67940

Other (OTH) AF: 0.570 AC: 1206 AN: 2114

Alfa AF: 0.539 Hom.: 11641

Bravo AF: 0.577

Asia WGS AF: 0.344 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs766325; hg19: chr1-18956458;