6-78415318-C-A

Variant names:

• chr6-78415318-C-A
• rs236233

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;