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. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000248973 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000248973	ENST00000847489.1	n.348+80685C>T		intron_variant	Intron 3 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

African (AFR) AF: 0.827 AC: 34307 AN: 41508

American (AMR) AF: 0.729 AC: 11134 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3181 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3358 AN: 5156

South Asian (SAS) AF: 0.842 AC: 4063 AN: 4826

European-Finnish (FIN) AF: 0.792 AC: 8375 AN: 10580

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57182 AN: 68002

Other (OTH) AF: 0.839 AC: 1772 AN: 2112

Alfa AF: 0.799 Hom.: 5270

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
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1393122; hg19: chr5-4725148;