6-27210249-T-C

Position:

• chr6-27210249-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 0.894 in 152,200 control chromosomes in the GnomAD database, including 61,094 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 0.89 (61094 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136039 AN: 152082 Hom.: 61059 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.894 AC: 136130 AN: 152200 Hom.: 61094 Cov.: 32 AF XY: 0.892 AC XY: 66333 AN XY: 74398

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.940

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.922

Alfa AF: 0.914 Hom.: 113994

Bravo AF: 0.903

Asia WGS AF: 0.964 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs858985; hg19: chr6-27178028;