1-28810174-A-G

Variant names:

• chr1-28810174-A-G
• rs569356
• ENST00000814652.1:n.91+13727A>G

Variant summary

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

The ENST00000814652.1(ENSG00000305996):​n.91+13727A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 152,110 control chromosomes in the GnomAD database, including 918 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 0.095 (918 hom., cov: 30)
• Consequence: ENSG00000305996 ENST00000814652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 36 publications found

Genes affected

ENSG00000305996 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814652.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305996	ENST00000814652.1		n.91+13727A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0954 AC: 14497 AN: 151992 Hom.: 915 Cov.: 30

Gnomad AFR AF: 0.0351

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.0991

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0578

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0954 AC: 14507 AN: 152110 Hom.: 918 Cov.: 30 AF XY: 0.0944 AC XY: 7015 AN XY: 74342

African (AFR) AF: 0.0353 AC: 1466 AN: 41516

American (AMR) AF: 0.0990 AC: 1509 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0810 AC: 281 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5180

South Asian (SAS) AF: 0.0574 AC: 277 AN: 4826

European-Finnish (FIN) AF: 0.119 AC: 1263 AN: 10576

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9258 AN: 67984

Other (OTH) AF: 0.114 AC: 240 AN: 2108

Alfa AF: 0.115 Hom.: 1570

Bravo AF: 0.0928

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs569356; hg19: chr1-29136686;