chr4-89844062-C-T

Variant names:

• chr4-89844062-C-T
• rs2870028

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;