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).

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
ENSG00000273550	ENST00000618134.1	n.177+11788T>C		intron_variant	Intron 2 of 2	3
ENSG00000273550	ENST00000658907.1	n.82+29164T>C		intron_variant	Intron 2 of 2

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 v4.3

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;