rs3800406

chr6-35165297-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 0.0764 in 152,230 control chromosomes in the GnomAD database, including 601 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 0.076 (601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0765 AC: 11634 AN: 152112 Hom.: 601 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0764 AC: 11626 AN: 152230 Hom.: 601 Cov.: 32 AF XY: 0.0783 AC XY: 5827 AN XY: 74416

Gnomad4 AFR AF: 0.0202

Gnomad4 AMR AF: 0.0545

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.0153

Gnomad4 SAS AF: 0.0380

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0960 Hom.: 199

Bravo AF: 0.0650

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.4
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3800406; hg19: chr6-35133074;