rs3846898

chr6-45734375-G-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 0.381 in 151,476 control chromosomes in the GnomAD database, including 11,595 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 0.38 (11595 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 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: 0.381 AC: 57723 AN: 151360 Hom.: 11594 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.381 AC: 57749 AN: 151476 Hom.: 11595 Cov.: 33 AF XY: 0.385 AC XY: 28472 AN XY: 74024

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.383

Alfa AF: 0.420 Hom.: 13999

Bravo AF: 0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.8
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3846898; hg19: chr6-45702112;