4-89859751-C-T

Variant names:

• chr4-89859751-C-T
• rs6532194

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 0.234 in 148,956 control chromosomes in the GnomAD database, including 6,284 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 0.23 (6284 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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: 0.234 AC: 34826 AN: 148920 Hom.: 6274 Cov.: 30

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.221

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.234 AC: 34840 AN: 148956 Hom.: 6284 Cov.: 30 AF XY: 0.237 AC XY: 17220 AN XY: 72524

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.0874

Gnomad4 OTH AF: 0.243

Alfa AF: 0.110 Hom.: 2699

Bravo AF: 0.258

Asia WGS AF: 0.415 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6532194; hg19: chr4-90780902;