chr13-63060217-G-T

Variant names:

• chr13-63060217-G-T
• rs9317284
• ENST00000618134.1:n.177+7809G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000618134.1(ENSG00000273550):​n.177+7809G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0524 in 151,016 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.052 (0 hom., cov: 60)
• Consequence: ENSG00000273550 ENST00000618134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 8 publications found

Genes affected

ENSG00000273550 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Variant has high frequency in the NFE (0.0686) population. However there is too low homozygotes in high coverage region: (expected more than 103, got 0).
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000618134.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273550	ENST00000618134.1	TSL:3	n.177+7809G>T		intron	N/A
	ENSG00000273550	ENST00000658907.1		n.82+25185G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0525 AC: 7917 AN: 150898 Hom.: 0 Cov.: 60

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0638

Gnomad ASJ AF: 0.0659

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.0880

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0524 AC: 7911 AN: 151016 Hom.: 0 Cov.: 60 AF XY: 0.0532 AC XY: 3929 AN XY: 73796

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0115 AC: 478 AN: 41478

American (AMR) AF: 0.0637 AC: 965 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.0659 AC: 227 AN: 3444

East Asian (EAS) AF: 0.0504 AC: 260 AN: 5162

South Asian (SAS) AF: 0.0431 AC: 207 AN: 4806

European-Finnish (FIN) AF: 0.0880 AC: 921 AN: 10464

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0703 AC: 4726 AN: 67224

Other (OTH) AF: 0.0449 AC: 94 AN: 2094

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.104 Hom.: 154

Bravo AF: 0.0944

Asia WGS AF: 0.0690 AC: 239 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.33
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9317284; hg19: chr13-63634350;