6-16109955-C-T

Position:

• chr6-16109955-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 0.637 in 152,046 control chromosomes in the GnomAD database, including 33,331 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 0.64 (33331 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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: 0.637 AC: 96733 AN: 151928 Hom.: 33270 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.637 AC: 96849 AN: 152046 Hom.: 33331 Cov.: 32 AF XY: 0.635 AC XY: 47212 AN XY: 74298

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.593

Alfa AF: 0.544 Hom.: 4894

Bravo AF: 0.662

Asia WGS AF: 0.816 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6913929; hg19: chr6-16110186;