chr6-153966897-G-A

Variant names:

• chr6-153966897-G-A
• rs6900805

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.890 AC: 36960 AN: 41530

American (AMR) AF: 0.832 AC: 12728 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2322 AN: 3464

East Asian (EAS) AF: 0.756 AC: 3901 AN: 5162

South Asian (SAS) AF: 0.791 AC: 3809 AN: 4818

European-Finnish (FIN) AF: 0.823 AC: 8700 AN: 10568

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50707 AN: 68004

Other (OTH) AF: 0.780 AC: 1648 AN: 2114

Alfa AF: 0.757 Hom.: 187569

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs6900805; hg19: chr6-154288032;