rs1892121

Variant names:

• chr1-224830399-A-G
• rs1892121
• ENST00000657178.1:n.78-9411T>C

Variant summary

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

The ENST00000657178.1(ENSG00000286719):​n.78-9411T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,174 control chromosomes in the GnomAD database, including 63,885 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 0.91 (63885 hom., cov: 30)
• Consequence: ENSG00000286719 ENST00000657178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 3 publications found

Genes affected

ENSG00000286719 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 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
ENSG00000286719	ENST00000657178.1	n.78-9411T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139058 AN: 152056 Hom.: 63831 Cov.: 30

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.915 AC: 139171 AN: 152174 Hom.: 63885 Cov.: 30 AF XY: 0.909 AC XY: 67646 AN XY: 74380

African (AFR) AF: 0.961 AC: 39920 AN: 41538

American (AMR) AF: 0.836 AC: 12779 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3219 AN: 3472

East Asian (EAS) AF: 0.763 AC: 3924 AN: 5144

South Asian (SAS) AF: 0.809 AC: 3882 AN: 4798

European-Finnish (FIN) AF: 0.910 AC: 9642 AN: 10596

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62801 AN: 68012

Other (OTH) AF: 0.912 AC: 1928 AN: 2114

Alfa AF: 0.915 Hom.: 10832

Bravo AF: 0.910

Asia WGS AF: 0.794 AC: 2760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.70
DANN	Benign	0.57
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1892121; hg19: chr1-225018101;