chr6-110506679-C-T

Variant names:

• chr6-110506679-C-T
• rs9481083

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 0.272 in 152,080 control chromosomes in the GnomAD database, including 6,357 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 0.27 (6357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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: 0.272 AC: 41342 AN: 151962 Hom.: 6345 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.272 AC: 41379 AN: 152080 Hom.: 6357 Cov.: 32 AF XY: 0.263 AC XY: 19531 AN XY: 74330

African (AFR) AF: 0.389 AC: 16122 AN: 41450

American (AMR) AF: 0.222 AC: 3392 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1391 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.133 AC: 640 AN: 4820

European-Finnish (FIN) AF: 0.157 AC: 1658 AN: 10574

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17171 AN: 67980

Other (OTH) AF: 0.286 AC: 606 AN: 2116

Alfa AF: 0.262 Hom.: 4588

Bravo AF: 0.286

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.44
DANN	Benign	0.52
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9481083; hg19: chr6-110827882;