6-83531146-T-C

Variant names:

• chr6-83531146-T-C
• rs1171105

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 0.7 in 151,862 control chromosomes in the GnomAD database, including 37,398 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 0.70 (37398 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106223 AN: 151746 Hom.: 37365 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.700 AC: 106310 AN: 151862 Hom.: 37398 Cov.: 31 AF XY: 0.701 AC XY: 52012 AN XY: 74232

African (AFR) AF: 0.761 AC: 31543 AN: 41432

American (AMR) AF: 0.627 AC: 9556 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3468

East Asian (EAS) AF: 0.632 AC: 3259 AN: 5158

South Asian (SAS) AF: 0.781 AC: 3757 AN: 4812

European-Finnish (FIN) AF: 0.696 AC: 7331 AN: 10530

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.685 AC: 46552 AN: 67916

Other (OTH) AF: 0.662 AC: 1396 AN: 2108

Alfa AF: 0.645 Hom.: 2829

Bravo AF: 0.691

Asia WGS AF: 0.702 AC: 2439 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.82
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs1171105; hg19: chr6-84240865;