6-115851928-C-G

Position:

• chr6-115851928-C-G

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 0.343 in 149,392 control chromosomes in the GnomAD database, including 9,077 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 0.34 (9077 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.115851928C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.343 AC: 51175 AN: 149288 Hom.: 9066 Cov.: 29

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.343 AC: 51220 AN: 149392 Hom.: 9077 Cov.: 29 AF XY: 0.343 AC XY: 24949 AN XY: 72694

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.385

Alfa AF: 0.318 Hom.: 992

Bravo AF: 0.361

Asia WGS AF: 0.343 AC: 1192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs195478; hg19: chr6-116173092;