rs62380518

Variant names:

• chr5-63689240-G-A
• rs62380518
• ENST00000722712.1:n.391+8565C>T

Variant summary

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

The ENST00000722712.1(ENSG00000294317):​n.391+8565C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 152,170 control chromosomes in the GnomAD database, including 790 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 0.091 (790 hom., cov: 32)
• Consequence: ENSG00000294317 ENST00000722712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

Genes affected

ENSG00000294317 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722712.1. 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
	ENSG00000294317	ENST00000722712.1		n.391+8565C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0914 AC: 13904 AN: 152050 Hom.: 791 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0896

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0914 AC: 13903 AN: 152170 Hom.: 790 Cov.: 32 AF XY: 0.0884 AC XY: 6576 AN XY: 74378

African (AFR) AF: 0.0375 AC: 1558 AN: 41544

American (AMR) AF: 0.0917 AC: 1402 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3470

East Asian (EAS) AF: 0.0192 AC: 99 AN: 5156

South Asian (SAS) AF: 0.0593 AC: 286 AN: 4824

European-Finnish (FIN) AF: 0.0896 AC: 948 AN: 10584

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.130 AC: 8861 AN: 67988

Other (OTH) AF: 0.109 AC: 229 AN: 2110

Alfa AF: 0.105 Hom.: 130

Bravo AF: 0.0915

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.66
PhyloP100		0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs62380518;

hg19: chr5-62985067;