rs1073203

Variant names:

• chr5-125983763-C-G
• rs1073203
• ENST00000651847.1:n.396-6168G>C

Variant summary

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

The ENST00000651847.1(ENSG00000248752):​n.396-6168G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,918 control chromosomes in the GnomAD database, including 1,814 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 0.14 (1814 hom., cov: 32)
• Consequence: ENSG00000248752 ENST00000651847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 9 publications found

Genes affected

ENSG00000248752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901056	XR_007058919.1	n.1774+114244G>C		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248752	ENST00000651847.1	n.396-6168G>C		intron_variant	Intron 4 of 15
ENSG00000248752	ENST00000781630.1	n.244-3105G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21737 AN: 151800 Hom.: 1813 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0497

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.143 AC: 21755 AN: 151918 Hom.: 1814 Cov.: 32 AF XY: 0.139 AC XY: 10317 AN XY: 74276

African (AFR) AF: 0.209 AC: 8674 AN: 41456

American (AMR) AF: 0.114 AC: 1735 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3466

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0499 AC: 241 AN: 4826

European-Finnish (FIN) AF: 0.0888 AC: 942 AN: 10610

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9139 AN: 67814

Other (OTH) AF: 0.152 AC: 321 AN: 2112

Alfa AF: 0.133 Hom.: 803

Bravo AF: 0.150

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.30
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1073203; hg19: chr5-125319456;