1-226509828-C-G

Variant names:

• chr1-226509828-C-G
• rs1727029
• ENST00000773545.1:n.207+31804C>G

Variant summary

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

The ENST00000773545.1(ENSG00000300711):​n.207+31804C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,910 control chromosomes in the GnomAD database, including 8,307 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 0.33 (8307 hom., cov: 32)
• Consequence: ENSG00000300711 ENST00000773545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 2 publications found

Genes affected

ENSG00000300711 (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 (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773545.1. 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
	ENSG00000300711	ENST00000773545.1		n.207+31804C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49561 AN: 151790 Hom.: 8299 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.327 AC: 49625 AN: 151910 Hom.: 8307 Cov.: 32 AF XY: 0.330 AC XY: 24489 AN XY: 74260

African (AFR) AF: 0.325 AC: 13463 AN: 41412

American (AMR) AF: 0.312 AC: 4774 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3470

East Asian (EAS) AF: 0.499 AC: 2570 AN: 5154

South Asian (SAS) AF: 0.495 AC: 2384 AN: 4818

European-Finnish (FIN) AF: 0.281 AC: 2958 AN: 10540

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21144 AN: 67926

Other (OTH) AF: 0.337 AC: 709 AN: 2104

Alfa AF: 0.307 Hom.: 917

Bravo AF: 0.326

Asia WGS AF: 0.482 AC: 1675 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	14
DANN	Benign	0.73
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1727029; hg19: chr1-226697529;