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).

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

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 v4.3

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;