rs6813195

chr4-152599323-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 0.342 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;