rs1120265

chr4-68671126-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.42 (10199 hom., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00 AC: 43202 AN: 103856 Hom.: 10177 Cov.: 19 FAILED QC

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.412

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: AS_VQSR AF: 0.416 AC: 43241 AN: 103912 Hom.: 10199 Cov.: 19 AF XY: 0.407 AC XY: 20046 AN XY: 49256

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.408

Alfa AF: 0.477 Hom.: 2105

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.6
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1120265; hg19: chr4-69536844; COSMIC: COSV57733324;