rs2478878

Variant names:

• chr6-51432679-G-C
• rs2478878

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 0.531 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
• Publications: 1 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 = 0.675 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.494 AC: 20384 AN: 41272

American (AMR) AF: 0.686 AC: 10423 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2142 AN: 3466

East Asian (EAS) AF: 0.687 AC: 3522 AN: 5130

South Asian (SAS) AF: 0.530 AC: 2544 AN: 4800

European-Finnish (FIN) AF: 0.527 AC: 5507 AN: 10452

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34003 AN: 67860

Other (OTH) AF: 0.577 AC: 1213 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.15
DANN	Benign	0.39
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2478878; hg19: chr6-51297477;