rs3846898

Variant names:

• chr6-45734375-G-T
• rs3846898

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;