rs3869062

Variant names:

• chr6-29967114-A-G
• rs3869062

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 0.0579 in 143,480 control chromosomes in the GnomAD database, including 454 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 0.058 (454 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

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 (EAS) allele frequency at 95% confidence interval = 0.252 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: 0.0579 AC: 8305 AN: 143364 Hom.: 452 Cov.: 33

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0572

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.0574

Gnomad NFE AF: 0.0639

Gnomad OTH AF: 0.0575

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

GnomAD4 genome AF: 0.0579 AC: 8305 AN: 143480 Hom.: 454 Cov.: 33 AF XY: 0.0612 AC XY: 4287 AN XY: 70070

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0471

Gnomad4 ASJ AF: 0.0572

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0587

Gnomad4 NFE AF: 0.0639

Gnomad4 OTH AF: 0.0585

Alfa AF: 0.0568 Hom.: 172

Bravo AF: 0.0508

Asia WGS AF: 0.162 AC: 556 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3869062; hg19: chr6-29934891;