6-27260521-T-G

Variant names:

• chr6-27260521-T-G
• rs9368493

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 0.118 in 152,162 control chromosomes in the GnomAD database, including 1,236 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 0.12 (1236 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828
• 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 (AFR) allele frequency at 95% confidence interval = 0.135 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: 0.118 AC: 17884 AN: 152044 Hom.: 1235 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.118 AC: 17891 AN: 152162 Hom.: 1236 Cov.: 31 AF XY: 0.122 AC XY: 9053 AN XY: 74376

African (AFR) AF: 0.138 AC: 5740 AN: 41508

American (AMR) AF: 0.0809 AC: 1236 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0761 AC: 264 AN: 3468

East Asian (EAS) AF: 0.115 AC: 595 AN: 5164

South Asian (SAS) AF: 0.0783 AC: 378 AN: 4826

European-Finnish (FIN) AF: 0.223 AC: 2359 AN: 10582

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

European-Non Finnish (NFE) AF: 0.102 AC: 6963 AN: 68014

Other (OTH) AF: 0.116 AC: 246 AN: 2116

Alfa AF: 0.0404 Hom.: 46

Bravo AF: 0.109

Asia WGS AF: 0.0820 AC: 286 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	6.7
DANN	Benign	0.27
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs9368493; hg19: chr6-27228300;