6-34227089-C-T

Variant names:

• chr6-34227089-C-T
• rs1759645

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 0.713 in 152,024 control chromosomes in the GnomAD database, including 41,089 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 0.71 (41089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.87 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: 0.713 AC: 108348 AN: 151906 Hom.: 41089 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.713 AC: 108381 AN: 152024 Hom.: 41089 Cov.: 32 AF XY: 0.718 AC XY: 53396 AN XY: 74328

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.892

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.716

Alfa AF: 0.807 Hom.: 45704

Bravo AF: 0.679

Asia WGS AF: 0.809 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1759645; hg19: chr6-34194866;