6-27210249-T-C

Variant names:

• chr6-27210249-T-C
• rs858985

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;