6-78415318-C-A

Position:

• chr6-78415318-C-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 0.802 in 152,024 control chromosomes in the GnomAD database, including 49,165 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 0.80 (49165 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78415318C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121854 AN: 151904 Hom.: 49118 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.802 AC: 121961 AN: 152024 Hom.: 49165 Cov.: 31 AF XY: 0.802 AC XY: 59615 AN XY: 74298

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.784

Alfa AF: 0.783 Hom.: 73952

Bravo AF: 0.803

Asia WGS AF: 0.865 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.89
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs236233; hg19: chr6-79125035;