1-119447230-A-G

Variant names:

• chr1-119447230-A-G
• rs1538989
• ENST00000632456.2:n.769-12083T>C

Variant summary

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

The ENST00000756944.1(ENSG00000293080):​n.340-12083T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,106 control chromosomes in the GnomAD database, including 16,092 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 (16092 hom., cov: 33)
• Consequence: ENSG00000293080 ENST00000756944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 7 publications found

Genes affected

ENSG00000293080 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756944.1. 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
	ENSG00000293080	ENST00000632456.2	TSL:6	n.769-12083T>C		intron	N/A
	ENSG00000293080	ENST00000756944.1		n.340-12083T>C		intron	N/A
	ENSG00000293080	ENST00000756945.1		n.519-12083T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64851 AN: 151988 Hom.: 16092 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.426 AC: 64853 AN: 152106 Hom.: 16092 Cov.: 33 AF XY: 0.429 AC XY: 31925 AN XY: 74334

African (AFR) AF: 0.162 AC: 6712 AN: 41514

American (AMR) AF: 0.508 AC: 7769 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1373 AN: 3472

East Asian (EAS) AF: 0.429 AC: 2215 AN: 5164

South Asian (SAS) AF: 0.385 AC: 1855 AN: 4820

European-Finnish (FIN) AF: 0.611 AC: 6456 AN: 10572

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36918 AN: 67964

Other (OTH) AF: 0.425 AC: 899 AN: 2116

Alfa AF: 0.481 Hom.: 2557

Bravo AF: 0.410

Asia WGS AF: 0.397 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.54
PhyloP100		-0.066

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1538989;

hg19: chr1-119989853;