rs1120265

Variant names:

• chr4-68671126-C-T
• rs1120265

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 3 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.416 AC: 43202 AN: 103856 Hom.: 10177 Cov.: 19

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

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

African (AFR) AF: 0.471 AC: 12687 AN: 26946

American (AMR) AF: 0.458 AC: 4461 AN: 9742

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 899 AN: 2512

East Asian (EAS) AF: 0.481 AC: 1773 AN: 3684

South Asian (SAS) AF: 0.322 AC: 1076 AN: 3344

European-Finnish (FIN) AF: 0.405 AC: 2573 AN: 6348

Middle Eastern (MID) AF: 0.423 AC: 104 AN: 246

European-Non Finnish (NFE) AF: 0.384 AC: 18829 AN: 49014

Other (OTH) AF: 0.408 AC: 580 AN: 1420

⚠️ 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: 0.477 Hom.: 2105

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.30
PhyloP100		-0.23
PromoterAI		0.0054	Neutral

Splicing

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

Other links and lift over

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