6-27259186-T-G

Variant names:

• chr6-27259186-T-G
• rs9393796

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 0.117 in 152,082 control chromosomes in the GnomAD database, including 1,233 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 (1233 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 10 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 = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17851 AN: 151964 Hom.: 1232 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.117 AC: 17858 AN: 152082 Hom.: 1233 Cov.: 31 AF XY: 0.122 AC XY: 9037 AN XY: 74326

African (AFR) AF: 0.138 AC: 5731 AN: 41470

American (AMR) AF: 0.0807 AC: 1235 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0761 AC: 264 AN: 3470

East Asian (EAS) AF: 0.115 AC: 593 AN: 5172

South Asian (SAS) AF: 0.0775 AC: 373 AN: 4814

European-Finnish (FIN) AF: 0.222 AC: 2338 AN: 10550

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

European-Non Finnish (NFE) AF: 0.102 AC: 6969 AN: 67996

Other (OTH) AF: 0.116 AC: 245 AN: 2110

Alfa AF: 0.102 Hom.: 2679

Bravo AF: 0.109

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.80
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs9393796; hg19: chr6-27226965;