1-75105994-A-G

Variant names:

• chr1-75105994-A-G
• rs1007512
• ENST00000794292.1:n.397-16811T>C

Variant summary

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

The ENST00000794292.1(ENSG00000303412):​n.397-16811T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,132 control chromosomes in the GnomAD database, including 5,143 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 0.23 (5143 hom., cov: 32)
• Consequence: ENSG00000303412 ENST00000794292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 3 publications found

Genes affected

ENSG00000303412 (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 (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794292.1. 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
	ENSG00000303412	ENST00000794292.1		n.397-16811T>C		intron	N/A
	ENSG00000303412	ENST00000794293.1		n.397-16811T>C		intron	N/A
	ENSG00000303412	ENST00000794294.1		n.523+6753T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34371 AN: 152016 Hom.: 5141 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.226 AC: 34386 AN: 152132 Hom.: 5143 Cov.: 32 AF XY: 0.236 AC XY: 17536 AN XY: 74366

African (AFR) AF: 0.113 AC: 4709 AN: 41526

American (AMR) AF: 0.334 AC: 5104 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3470

East Asian (EAS) AF: 0.766 AC: 3945 AN: 5150

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4826

European-Finnish (FIN) AF: 0.275 AC: 2907 AN: 10584

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14861 AN: 67984

Other (OTH) AF: 0.243 AC: 515 AN: 2116

Alfa AF: 0.181 Hom.: 750

Bravo AF: 0.228

Asia WGS AF: 0.484 AC: 1684 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.4
DANN	Benign	0.72
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1007512; hg19: chr1-75571679;