rs6878378

Variant names:

• chr5-163618938-C-T
• rs6878378

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 0.206 in 152,106 control chromosomes in the GnomAD database, including 4,003 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 0.21 (4003 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 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: 0.206 AC: 31313 AN: 151988 Hom.: 4000 Cov.: 33

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.206 AC: 31354 AN: 152106 Hom.: 4003 Cov.: 33 AF XY: 0.202 AC XY: 15010 AN XY: 74380

African (AFR) AF: 0.362 AC: 15014 AN: 41452

American (AMR) AF: 0.160 AC: 2452 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3470

East Asian (EAS) AF: 0.133 AC: 687 AN: 5176

South Asian (SAS) AF: 0.175 AC: 845 AN: 4820

European-Finnish (FIN) AF: 0.120 AC: 1267 AN: 10602

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9803 AN: 67978

Other (OTH) AF: 0.206 AC: 434 AN: 2108

Alfa AF: 0.164 Hom.: 9565

Bravo AF: 0.216

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.41
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs6878378; hg19: chr5-163045944; COSMIC: COSV107163814;