1-162891123-A-G

Variant names:

• chr1-162891123-A-G
• rs4412572
• ENST00000772589.1:n.42+12842A>G

Variant summary

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

The ENST00000772589.1(ENSG00000300530):​n.42+12842A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,102 control chromosomes in the GnomAD database, including 47,788 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 0.77 (47788 hom., cov: 31)
• Consequence: ENSG00000300530 ENST00000772589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232
• Publications: 5 publications found

Genes affected

ENSG00000300530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 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
ENSG00000300530	ENST00000772589.1	n.42+12842A>G		intron_variant	Intron 1 of 2
ENSG00000300530	ENST00000772590.1	n.80+12801A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117616 AN: 151984 Hom.: 47787 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.774 AC: 117666 AN: 152102 Hom.: 47788 Cov.: 31 AF XY: 0.771 AC XY: 57296 AN XY: 74354

African (AFR) AF: 0.549 AC: 22745 AN: 41442

American (AMR) AF: 0.760 AC: 11602 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3104 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2191 AN: 5158

South Asian (SAS) AF: 0.734 AC: 3539 AN: 4824

European-Finnish (FIN) AF: 0.928 AC: 9838 AN: 10598

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61986 AN: 68014

Other (OTH) AF: 0.798 AC: 1688 AN: 2116

Alfa AF: 0.872 Hom.: 101535

Bravo AF: 0.750

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.41
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4412572; hg19: chr1-162860913;