XR_007066809.1:n.282-8369C>T

Variant names:

• chr1-203523592-C-T
• rs13303128
• ENST00000760074.1:n.572C>T

Variant summary

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

The XR_007066809.1(LOC124904488):​n.282-8369C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,008 control chromosomes in the GnomAD database, including 34,848 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 0.67 (34848 hom., cov: 31)
• Consequence: LOC124904488 XR_007066809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 2 publications found

Genes affected

ENSG00000299041 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000760074.1. 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
	ENSG00000299041	ENST00000760074.1		n.572C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000299041	ENST00000760072.1		n.306+142C>T		intron	N/A
	ENSG00000299041	ENST00000760073.1		n.360+142C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102375 AN: 151890 Hom.: 34795 Cov.: 31

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.674 AC: 102497 AN: 152008 Hom.: 34848 Cov.: 31 AF XY: 0.676 AC XY: 50228 AN XY: 74322

African (AFR) AF: 0.766 AC: 31762 AN: 41444

American (AMR) AF: 0.733 AC: 11197 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2242 AN: 3470

East Asian (EAS) AF: 0.595 AC: 3081 AN: 5174

South Asian (SAS) AF: 0.608 AC: 2926 AN: 4812

European-Finnish (FIN) AF: 0.642 AC: 6785 AN: 10570

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42313 AN: 67952

Other (OTH) AF: 0.645 AC: 1363 AN: 2114

Alfa AF: 0.652 Hom.: 4016

Bravo AF: 0.687

Asia WGS AF: 0.626 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.88
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs13303128; hg19: chr1-203492720; COSMIC: COSV60018510;