6-27719256-C-T

Variant names:

• chr6-27719256-C-T
• rs9468201

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 0.299 in 151,830 control chromosomes in the GnomAD database, including 7,664 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 0.30 (7664 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 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: 0.298 AC: 45282 AN: 151710 Hom.: 7649 Cov.: 31

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.299 AC: 45342 AN: 151830 Hom.: 7664 Cov.: 31 AF XY: 0.294 AC XY: 21790 AN XY: 74198

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.283

Alfa AF: 0.142 Hom.: 255

Bravo AF: 0.313

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9468201; hg19: chr6-27687035;