1-182013826-A-C

Variant names:

• chr1-182013826-A-C
• rs2877815
• ENST00000757171.1:n.272-10681T>G

Variant summary

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

The ENST00000757171.1(ENSG00000298667):​n.272-10681T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,086 control chromosomes in the GnomAD database, including 3,804 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 (3804 hom., cov: 32)
• Consequence: ENSG00000298667 ENST00000757171.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 0 publications found

Genes affected

ENSG00000298667 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757171.1. 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
	ENSG00000298667	ENST00000757171.1		n.272-10681T>G		intron	N/A
	ENSG00000298667	ENST00000757172.1		n.541+8348T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30331 AN: 151968 Hom.: 3803 Cov.: 32

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0119

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.199 AC: 30322 AN: 152086 Hom.: 3804 Cov.: 32 AF XY: 0.196 AC XY: 14608 AN XY: 74344

African (AFR) AF: 0.0609 AC: 2526 AN: 41502

American (AMR) AF: 0.219 AC: 3339 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3464

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5182

South Asian (SAS) AF: 0.135 AC: 650 AN: 4828

European-Finnish (FIN) AF: 0.263 AC: 2777 AN: 10558

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19014 AN: 67970

Other (OTH) AF: 0.230 AC: 485 AN: 2106

Alfa AF: 0.217 Hom.: 1062

Bravo AF: 0.191

Asia WGS AF: 0.0700 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.81
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2877815; hg19: chr1-181982961;