rs2378627

Variant names:

• chr1-223058670-A-G
• rs2378627
• ENST00000789333.1:n.265-4443A>G

Variant summary

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

The ENST00000789333.1(ENSG00000302753):​n.265-4443A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,098 control chromosomes in the GnomAD database, including 8,677 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 (8677 hom., cov: 32)
• Consequence: ENSG00000302753 ENST00000789333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86
• Publications: 0 publications found

Genes affected

ENSG00000302753 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789333.1. 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
	ENSG00000302753	ENST00000789333.1		n.265-4443A>G		intron	N/A
	ENSG00000302753	ENST00000789335.1		n.315-4443A>G		intron	N/A
	ENSG00000302753	ENST00000789336.1		n.169-4443A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50516 AN: 151980 Hom.: 8666 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.333 AC: 50577 AN: 152098 Hom.: 8677 Cov.: 32 AF XY: 0.332 AC XY: 24659 AN XY: 74336

African (AFR) AF: 0.290 AC: 12026 AN: 41498

American (AMR) AF: 0.295 AC: 4514 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1554 AN: 5164

South Asian (SAS) AF: 0.375 AC: 1809 AN: 4818

European-Finnish (FIN) AF: 0.370 AC: 3902 AN: 10558

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24598 AN: 67994

Other (OTH) AF: 0.312 AC: 659 AN: 2112

Alfa AF: 0.352 Hom.: 1189

Bravo AF: 0.324

Asia WGS AF: 0.326 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.24
DANN	Benign	0.13
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs2378627; hg19: chr1-223232012;