rs1766581

Variant names:

• chr1-232311547-C-T
• rs1766581
• ENST00000808822.1:n.374+1175G>A

Variant summary

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

The ENST00000808822.1(ENSG00000305110):​n.374+1175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,028 control chromosomes in the GnomAD database, including 11,328 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 0.37 (11328 hom., cov: 32)
• Consequence: ENSG00000305110 ENST00000808822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 6 publications found

Genes affected

ENSG00000305110 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808822.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305110	ENST00000808822.1		n.374+1175G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56667 AN: 151910 Hom.: 11331 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.373 AC: 56693 AN: 152028 Hom.: 11328 Cov.: 32 AF XY: 0.369 AC XY: 27407 AN XY: 74336

African (AFR) AF: 0.252 AC: 10442 AN: 41478

American (AMR) AF: 0.365 AC: 5575 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1586 AN: 3464

East Asian (EAS) AF: 0.216 AC: 1115 AN: 5164

South Asian (SAS) AF: 0.456 AC: 2199 AN: 4820

European-Finnish (FIN) AF: 0.347 AC: 3662 AN: 10562

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30697 AN: 67948

Other (OTH) AF: 0.403 AC: 851 AN: 2114

Alfa AF: 0.327 Hom.: 1535

Bravo AF: 0.367

Asia WGS AF: 0.324 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.096
DANN	Benign	0.60
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1766581; hg19: chr1-232447293; COSMIC: COSV60038751;