6-165226528-C-T

Variant names:

• chr6-165226528-C-T
• rs16897566

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 0.131 in 152,072 control chromosomes in the GnomAD database, including 1,402 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 0.13 (1402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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: 0.131 AC: 19857 AN: 151954 Hom.: 1392 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.0724

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.131 AC: 19898 AN: 152072 Hom.: 1402 Cov.: 32 AF XY: 0.130 AC XY: 9669 AN XY: 74326

African (AFR) AF: 0.136 AC: 5642 AN: 41482

American (AMR) AF: 0.176 AC: 2686 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 383 AN: 3466

East Asian (EAS) AF: 0.253 AC: 1303 AN: 5154

South Asian (SAS) AF: 0.0722 AC: 348 AN: 4818

European-Finnish (FIN) AF: 0.117 AC: 1235 AN: 10572

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7955 AN: 67986

Other (OTH) AF: 0.131 AC: 276 AN: 2114

Alfa AF: 0.119 Hom.: 2267

Bravo AF: 0.137

Asia WGS AF: 0.161 AC: 557 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	0.33
DANN	Benign	0.63
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs16897566; hg19: chr6-165640017;