chr4-68671124-A-T

Variant names:

• chr4-68671124-A-T
• rs1580083

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 (10298 hom., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.417 AC: 43502 AN: 104316 Hom.: 10278 Cov.: 19

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.415

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: 0.417 AC: 43535 AN: 104362 Hom.: 10298 Cov.: 19 AF XY: 0.408 AC XY: 20182 AN XY: 49516

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

African (AFR) AF: 0.471 AC: 12762 AN: 27102

American (AMR) AF: 0.461 AC: 4528 AN: 9822

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 905 AN: 2526

East Asian (EAS) AF: 0.481 AC: 1781 AN: 3700

South Asian (SAS) AF: 0.322 AC: 1089 AN: 3378

European-Finnish (FIN) AF: 0.404 AC: 2571 AN: 6366

Middle Eastern (MID) AF: 0.419 AC: 103 AN: 246

European-Non Finnish (NFE) AF: 0.386 AC: 18944 AN: 49128

Other (OTH) AF: 0.411 AC: 588 AN: 1430

⚠️ 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: 0.271 Hom.: 597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.38
PhyloP100		-0.041
PromoterAI		0.0081	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1580083; hg19: chr4-69536842; COSMIC: COSV57733319;