rs2478878

Variant names:

• chr6-51432679-G-C
• rs2478878

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 0.531 in 151,478 control chromosomes in the GnomAD database, including 21,681 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 0.53 (21681 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -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 = 0.675 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: 0.531 AC: 80297 AN: 151360 Hom.: 21654 Cov.: 29

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.531 AC: 80368 AN: 151478 Hom.: 21681 Cov.: 29 AF XY: 0.536 AC XY: 39601 AN XY: 73944

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.577

Alfa AF: 0.517 Hom.: 2591

Bravo AF: 0.543

Asia WGS AF: 0.607 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.15
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2478878; hg19: chr6-51297477;