chr6-17755653-T-C

Position:

• chr6-17755653-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 0.578 in 152,040 control chromosomes in the GnomAD database, including 25,646 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 0.58 (25646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 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: 0.578 AC: 87784 AN: 151922 Hom.: 25621 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.578 AC: 87853 AN: 152040 Hom.: 25646 Cov.: 32 AF XY: 0.579 AC XY: 43029 AN XY: 74312

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.603

Alfa AF: 0.594 Hom.: 34984

Bravo AF: 0.576

Asia WGS AF: 0.693 AC: 2411 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	0.54
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9396802; hg19: chr6-17755884;