1-172674080-A-G

Variant names:

• chr1-172674080-A-G
• rs2021840
• ENST00000725727.1:n.69+3481A>G

Variant summary

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

The ENST00000725727.1(ENSG00000224000):​n.69+3481A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,082 control chromosomes in the GnomAD database, including 5,425 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 0.26 (5425 hom., cov: 31)
• Consequence: ENSG00000224000 ENST00000725727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 10 publications found

Genes affected

ENSG00000224000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224000	ENST00000725727.1	n.69+3481A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39135 AN: 151964 Hom.: 5407 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.258 AC: 39196 AN: 152082 Hom.: 5425 Cov.: 31 AF XY: 0.255 AC XY: 18939 AN XY: 74336

African (AFR) AF: 0.280 AC: 11599 AN: 41466

American (AMR) AF: 0.241 AC: 3686 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1428 AN: 3470

East Asian (EAS) AF: 0.0999 AC: 517 AN: 5176

South Asian (SAS) AF: 0.392 AC: 1888 AN: 4812

European-Finnish (FIN) AF: 0.151 AC: 1603 AN: 10584

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17490 AN: 67978

Other (OTH) AF: 0.292 AC: 615 AN: 2104

Alfa AF: 0.270 Hom.: 8217

Bravo AF: 0.263

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.68
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2021840; hg19: chr1-172643220;