6-26556662-G-C

Position:

• chr6-26556662-G-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 0.0564 in 152,028 control chromosomes in the GnomAD database, including 408 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 0.056 (408 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.12 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: 0.0564 AC: 8565 AN: 151910 Hom.: 409 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0208

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0564 AC: 8577 AN: 152028 Hom.: 408 Cov.: 32 AF XY: 0.0577 AC XY: 4291 AN XY: 74338

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0251

Gnomad4 ASJ AF: 0.0184

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0347

Gnomad4 NFE AF: 0.0208

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0122 Hom.: 1

Bravo AF: 0.0565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	0.42
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484443; hg19: chr6-26556890;