chr4-152599323-C-T

Variant names:

• chr4-152599323-C-T
• rs6813195

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 0.342 in 151,884 control chromosomes in the GnomAD database, including 9,188 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 0.34 (9188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 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: 0.342 AC: 51919 AN: 151766 Hom.: 9169 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.342 AC: 51975 AN: 151884 Hom.: 9188 Cov.: 32 AF XY: 0.348 AC XY: 25809 AN XY: 74206

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.361

Alfa AF: 0.298 Hom.: 10902

Bravo AF: 0.348

Asia WGS AF: 0.440 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6813195; hg19: chr4-153520475;