rs6900805

chr6-153966897-G-Achr6-153966897-G-Cchr6-153966897-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 0.8 in 152,158 control chromosomes in the GnomAD database, including 49,081 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 0.80 (49081 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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: 0.800 AC: 121660 AN: 152040 Hom.: 49055 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.800 AC: 121734 AN: 152158 Hom.: 49081 Cov.: 32 AF XY: 0.803 AC XY: 59711 AN XY: 74380

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.780

Alfa AF: 0.747 Hom.: 86121

Bravo AF: 0.805

Asia WGS AF: 0.756 AC: 2631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.17
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: rs6900805; hg19: chr6-154288032;