rs1393467

Variant names:

• chr17-53483508-A-G
• rs1393467
• ENST00000650577.1:n.660-38434T>C

Variant summary

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

The ENST00000650577.1(ENSG00000285939):​n.660-38434T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0513 in 152,066 control chromosomes in the GnomAD database, including 306 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 0.051 (306 hom., cov: 32)
• Consequence: ENSG00000285939 ENST00000650577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 2 publications found

Genes affected

ENSG00000285939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650577.1. 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
	ENSG00000285939	ENST00000650577.1		n.660-38434T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0512 AC: 7787 AN: 151948 Hom.: 305 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0513 AC: 7802 AN: 152066 Hom.: 306 Cov.: 32 AF XY: 0.0507 AC XY: 3768 AN XY: 74330

African (AFR) AF: 0.111 AC: 4629 AN: 41532

American (AMR) AF: 0.0323 AC: 494 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3464

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5186

South Asian (SAS) AF: 0.0607 AC: 293 AN: 4826

European-Finnish (FIN) AF: 0.0171 AC: 181 AN: 10614

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0286 AC: 1941 AN: 67854

Other (OTH) AF: 0.0389 AC: 82 AN: 2110

Alfa AF: 0.0349 Hom.: 59

Bravo AF: 0.0553

Asia WGS AF: 0.0440 AC: 153 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.70
DANN	Benign	0.44
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1393467; hg19: chr17-51560869;