rs3920498

Variant names:

• chr1-22166394-G-C
• rs3920498
• ENST00000725701.1:n.125+2898G>C

Variant summary

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

The ENST00000725701.1(ENSG00000294752):​n.125+2898G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,180 control chromosomes in the GnomAD database, including 3,195 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 0.20 (3195 hom., cov: 32)
• Consequence: ENSG00000294752 ENST00000725701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.624
• Publications: 29 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 (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376850	XR_947057.3	n.154+2898G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294752	ENST00000725701.1	n.125+2898G>C		intron_variant	Intron 1 of 3
ENSG00000294752	ENST00000725702.1	n.125+2898G>C		intron_variant	Intron 1 of 2
ENSG00000294752	ENST00000725703.1	n.108+2898G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29874 AN: 152060 Hom.: 3186 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.197 AC: 29910 AN: 152180 Hom.: 3195 Cov.: 32 AF XY: 0.201 AC XY: 14979 AN XY: 74402

African (AFR) AF: 0.163 AC: 6772 AN: 41516

American (AMR) AF: 0.217 AC: 3327 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2353 AN: 5168

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4826

European-Finnish (FIN) AF: 0.210 AC: 2223 AN: 10592

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13084 AN: 67994

Other (OTH) AF: 0.165 AC: 350 AN: 2116

Alfa AF: 0.201 Hom.: 408

Bravo AF: 0.197

Asia WGS AF: 0.286 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.65
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs3920498; hg19: chr1-22492887;