6-108698120-C-A

Variant names:

• chr6-108698120-C-A
• rs473268

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.455 in 152,056 control chromosomes in the GnomAD database, including 17,842 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 0.45 (17842 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.591
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 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: 0.454 AC: 69045 AN: 151938 Hom.: 17807 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.455 AC: 69138 AN: 152056 Hom.: 17842 Cov.: 32 AF XY: 0.453 AC XY: 33711 AN XY: 74344

African (AFR) AF: 0.721 AC: 29882 AN: 41460

American (AMR) AF: 0.373 AC: 5707 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1081 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1382 AN: 5168

South Asian (SAS) AF: 0.413 AC: 1994 AN: 4828

European-Finnish (FIN) AF: 0.405 AC: 4284 AN: 10588

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23451 AN: 67936

Other (OTH) AF: 0.424 AC: 896 AN: 2112

Alfa AF: 0.428 Hom.: 2042

Bravo AF: 0.463

Asia WGS AF: 0.405 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.36
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs473268; hg19: chr6-109019323;