rs3893464

Variant names:

• chr6-29967473-G-A
• rs3893464

Your query was ambiguous. Multiple possible variants found:

• chr6-29967473-G-A
• chr6-29967473-G-C
• chr6-29967473-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 0.463 in 151,862 control chromosomes in the GnomAD database, including 16,681 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 0.46 (16681 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.63 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: 0.463 AC: 70200 AN: 151746 Hom.: 16659 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.463 AC: 70268 AN: 151862 Hom.: 16681 Cov.: 32 AF XY: 0.466 AC XY: 34600 AN XY: 74244

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.474

Alfa AF: 0.472 Hom.: 25926

Bravo AF: 0.459

Asia WGS AF: 0.653 AC: 2251 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3893464; hg19: chr6-29935250;