rs883062

Variant names:

• chr1-42144196-G-A
• rs883062
• ENST00000826366.1:n.159+3826C>T

Variant summary

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

The ENST00000826366.1(ENSG00000307448):​n.159+3826C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,138 control chromosomes in the GnomAD database, including 16,561 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 0.43 (16561 hom., cov: 32)
• Consequence: ENSG00000307448 ENST00000826366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 9 publications found

Genes affected

ENSG00000307448 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826366.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307448	ENST00000826366.1		n.159+3826C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65116 AN: 152020 Hom.: 16567 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.428 AC: 65118 AN: 152138 Hom.: 16561 Cov.: 32 AF XY: 0.428 AC XY: 31826 AN XY: 74386

African (AFR) AF: 0.138 AC: 5747 AN: 41524

American (AMR) AF: 0.497 AC: 7601 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2220 AN: 3466

East Asian (EAS) AF: 0.364 AC: 1885 AN: 5184

South Asian (SAS) AF: 0.439 AC: 2117 AN: 4824

European-Finnish (FIN) AF: 0.566 AC: 5989 AN: 10584

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37892 AN: 67954

Other (OTH) AF: 0.472 AC: 996 AN: 2108

Alfa AF: 0.527 Hom.: 36694

Bravo AF: 0.413

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.7
DANN	Benign	0.81
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs883062; hg19: chr1-42609867;