6-10886716-C-T

Position:

• chr6-10886716-C-T

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 0.829 in 214,190 control chromosomes in the GnomAD database, including 73,974 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 0.84 (53474 hom., cov: 34)
  • Exomes 𝑓: 0.81 (20500 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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: 0.837 AC: 127286 AN: 152118 Hom.: 53429 Cov.: 34

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.837

GnomAD4 exome AF: 0.809 AC: 50138 AN: 61954 Hom.: 20500 AF XY: 0.807 AC XY: 26336 AN XY: 32622

Gnomad4 AFR exome AF: 0.887

Gnomad4 AMR exome AF: 0.855

Gnomad4 ASJ exome AF: 0.824

Gnomad4 EAS exome AF: 0.662

Gnomad4 SAS exome AF: 0.789

Gnomad4 FIN exome AF: 0.795

Gnomad4 NFE exome AF: 0.820

Gnomad4 OTH exome AF: 0.824

GnomAD4 genome AF: 0.837 AC: 127391 AN: 152236 Hom.: 53474 Cov.: 34 AF XY: 0.834 AC XY: 62045 AN XY: 74434

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.837

Alfa AF: 0.823 Hom.: 33515

Bravo AF: 0.843

Asia WGS AF: 0.778 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9379896; hg19: chr6-10886949;