6-16109955-C-T

Variant names:

• chr6-16109955-C-T
• rs6913929

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;