chr6-116871027-G-A

Position:

• chr6-116871027-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 0.264 in 151,868 control chromosomes in the GnomAD database, including 5,496 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 0.26 (5496 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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: 0.264 AC: 40003 AN: 151748 Hom.: 5489 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.264 AC: 40043 AN: 151868 Hom.: 5496 Cov.: 32 AF XY: 0.269 AC XY: 19947 AN XY: 74242

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.230

Alfa AF: 0.263 Hom.: 1497

Bravo AF: 0.256

Asia WGS AF: 0.397 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs339321; hg19: chr6-117192190;