rs1393122

Variant names:

• chr5-4725035-G-A
• rs1393122
• ENST00000507435.1:n.429+59836C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-4725035-G-A
• chr5-4725035-G-C
• chr5-4725035-G-T

Variant summary

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

The ENST00000507435.1(ENSG00000248973):​n.429+59836C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,142 control chromosomes in the GnomAD database, including 51,167 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 0.82 (51167 hom., cov: 32)
• Consequence: ENSG00000248973 ENST00000507435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

ENSG00000248973 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248973	ENST00000507435.1	n.429+59836C>T		intron_variant	Intron 3 of 5	5
ENSG00000248973	ENST00000651524.1	n.212-17666C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124388 AN: 152024 Hom.: 51133 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.818 AC: 124475 AN: 152142 Hom.: 51167 Cov.: 32 AF XY: 0.812 AC XY: 60350 AN XY: 74364

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.839

Alfa AF: 0.796 Hom.: 4990

Bravo AF: 0.812

Asia WGS AF: 0.760 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.46
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1393122; hg19: chr5-4725148;