4-89844062-C-T

Position:

• chr4-89844062-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.305 in 151,724 control chromosomes in the GnomAD database, including 7,983 homozygotes. 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 0.31 (7983 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

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: 0.306 AC: 46323 AN: 151606 Hom.: 7988 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.285

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.305 AC: 46311 AN: 151724 Hom.: 7983 Cov.: 32 AF XY: 0.303 AC XY: 22449 AN XY: 74114

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.281

Alfa AF: 0.342 Hom.: 1205

Bravo AF: 0.287

Asia WGS AF: 0.233 AC: 810 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
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: rs2870028; hg19: chr4-90765213;