chr6-85171753-C-T

Variant names:

• chr6-85171753-C-T
• rs3966882

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 0.55 in 151,960 control chromosomes in the GnomAD database, including 23,879 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 0.55 (23879 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83496 AN: 151842 Hom.: 23874 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.550 AC: 83546 AN: 151960 Hom.: 23879 Cov.: 32 AF XY: 0.561 AC XY: 41656 AN XY: 74270

African (AFR) AF: 0.577 AC: 23910 AN: 41418

American (AMR) AF: 0.631 AC: 9642 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1813 AN: 3464

East Asian (EAS) AF: 0.941 AC: 4867 AN: 5172

South Asian (SAS) AF: 0.685 AC: 3300 AN: 4820

European-Finnish (FIN) AF: 0.582 AC: 6138 AN: 10548

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32216 AN: 67944

Other (OTH) AF: 0.521 AC: 1099 AN: 2110

Alfa AF: 0.505 Hom.: 15068

Bravo AF: 0.555

Asia WGS AF: 0.774 AC: 2687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs3966882; hg19: chr6-85881471;