4-68671124-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).

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: 0.417 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 v4.3

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;