chr6-16108932-A-C

Position:

• chr6-16108932-A-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 0.648 in 152,078 control chromosomes in the GnomAD database, including 34,279 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 0.65 (34279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.648 AC: 98482 AN: 151960 Hom.: 34219 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.648 AC: 98597 AN: 152078 Hom.: 34279 Cov.: 32 AF XY: 0.647 AC XY: 48069 AN XY: 74338

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.606

Alfa AF: 0.542 Hom.: 30348

Bravo AF: 0.673

Asia WGS AF: 0.818 AC: 2844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2294261; hg19: chr6-16109163;