6-16196963-G-A

Position:

• chr6-16196963-G-A

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 0.415 in 151,832 control chromosomes in the GnomAD database, including 15,871 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 0.42 (15871 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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: 0.415 AC: 62979 AN: 151714 Hom.: 15822 Cov.: 31

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.415 AC: 63086 AN: 151832 Hom.: 15871 Cov.: 31 AF XY: 0.412 AC XY: 30569 AN XY: 74216

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.369

Alfa AF: 0.296 Hom.: 12708

Bravo AF: 0.437

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2142672; hg19: chr6-16197194;