rs1073203

chr5-125983763-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651847.1(ENSG00000248752):n.396-6168G>C variant causes a intron, non coding transcript 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: ENST00000651847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124901056	XR_007058919.1	n.1774+114244G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651847.1	n.396-6168G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0499

Gnomad4 FIN AF: 0.0888

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.152

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1073203; hg19: chr5-125319456;