6-27281152-T-C

Position:

• chr6-27281152-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.253 in 148,938 control chromosomes in the GnomAD database, including 5,207 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 0.25 (5207 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.254 AC: 37732 AN: 148838 Hom.: 5200 Cov.: 29

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.289

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.253 AC: 37745 AN: 148938 Hom.: 5207 Cov.: 29 AF XY: 0.244 AC XY: 17732 AN XY: 72714

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0285

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.260

Alfa AF: 0.245 Hom.: 10585

Bravo AF: 0.265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6932590; hg19: chr6-27248931; COSMIC: COSV70387444;