rs3119939

Variant names:

• chr13-63064196-T-C
• rs3119939
• ENST00000618134.1:n.177+11788T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000618134.1(ENSG00000273550):​n.177+11788T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.27 (13 hom., cov: 72)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000273550 ENST00000618134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 6 publications found

Genes affected

ENSG00000273550 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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

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
	ENSG00000273550	ENST00000618134.1	TSL:3	n.177+11788T>C		intron	N/A
	ENSG00000273550	ENST00000658907.1		n.82+29164T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.267 AC: 34145 AN: 127808 Hom.: 13 Cov.: 72

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0180

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.267

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.267 AC: 34143 AN: 127924 Hom.: 13 Cov.: 72 AF XY: 0.261 AC XY: 16323 AN XY: 62530

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

African (AFR) AF: 0.214 AC: 7479 AN: 34956

American (AMR) AF: 0.244 AC: 3142 AN: 12852

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 885 AN: 2858

East Asian (EAS) AF: 0.0180 AC: 92 AN: 5112

South Asian (SAS) AF: 0.270 AC: 1092 AN: 4040

European-Finnish (FIN) AF: 0.244 AC: 2199 AN: 9010

Middle Eastern (MID) AF: 0.306 AC: 79 AN: 258

European-Non Finnish (NFE) AF: 0.328 AC: 18474 AN: 56338

Other (OTH) AF: 0.262 AC: 463 AN: 1764

⚠️ 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: 0.435 Hom.: 44164

Asia WGS AF: 0.207 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.6
DANN	Benign	0.68
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs3119939; hg19: chr13-63638329;