rs3869062

Positions:

• chr6-29967114-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;