6-112679456-C-A

Variant names:

• chr6-112679456-C-A
• rs1378702

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 0.691 in 151,964 control chromosomes in the GnomAD database, including 36,503 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 0.69 (36503 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.973
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104962 AN: 151846 Hom.: 36475 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.691 AC: 105041 AN: 151964 Hom.: 36503 Cov.: 32 AF XY: 0.692 AC XY: 51360 AN XY: 74254

African (AFR) AF: 0.722 AC: 29956 AN: 41470

American (AMR) AF: 0.711 AC: 10873 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2518 AN: 3468

East Asian (EAS) AF: 0.899 AC: 4653 AN: 5174

South Asian (SAS) AF: 0.681 AC: 3287 AN: 4826

European-Finnish (FIN) AF: 0.599 AC: 6310 AN: 10542

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45337 AN: 67886

Other (OTH) AF: 0.713 AC: 1500 AN: 2104

Alfa AF: 0.670 Hom.: 4270

Bravo AF: 0.702

Asia WGS AF: 0.786 AC: 2722 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.31
DANN	Benign	0.66
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs1378702; hg19: chr6-113000658;