chr1-22249447-C-G

Variant names:

• chr1-22249447-C-G
• rs875975
• ENST00000725701.1:n.412-23359C>G

Variant summary

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

The ENST00000725701.1(ENSG00000294752):​n.412-23359C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,162 control chromosomes in the GnomAD database, including 3,227 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 0.19 (3227 hom., cov: 33)
• Consequence: ENSG00000294752 ENST00000725701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 6 publications found

Genes affected

ENSG00000294752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725701.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294752	ENST00000725701.1		n.412-23359C>G		intron	N/A
	ENSG00000294752	ENST00000725702.1		n.236-23359C>G		intron	N/A
	ENSG00000294752	ENST00000725703.1		n.393+19367C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29354 AN: 152044 Hom.: 3226 Cov.: 33

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.193 AC: 29359 AN: 152162 Hom.: 3227 Cov.: 33 AF XY: 0.196 AC XY: 14562 AN XY: 74380

African (AFR) AF: 0.0845 AC: 3510 AN: 41552

American (AMR) AF: 0.210 AC: 3203 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1167 AN: 5142

South Asian (SAS) AF: 0.242 AC: 1165 AN: 4824

European-Finnish (FIN) AF: 0.271 AC: 2863 AN: 10582

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16159 AN: 67996

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.214 Hom.: 466

Bravo AF: 0.180

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.63
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs875975; hg19: chr1-22575940;