rs13278851

Variant names:

• chr8-9893362-G-A
• rs13278851

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 0.0877 in 152,180 control chromosomes in the GnomAD database, including 760 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 0.088 (760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.151 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: 0.0877 AC: 13332 AN: 152062 Hom.: 755 Cov.: 32

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0688

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0885

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

GnomAD4 genome AF: 0.0877 AC: 13349 AN: 152180 Hom.: 760 Cov.: 32 AF XY: 0.0906 AC XY: 6741 AN XY: 74374

African (AFR) AF: 0.0222 AC: 922 AN: 41534

American (AMR) AF: 0.120 AC: 1829 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0688 AC: 239 AN: 3472

East Asian (EAS) AF: 0.160 AC: 827 AN: 5156

South Asian (SAS) AF: 0.0898 AC: 433 AN: 4820

European-Finnish (FIN) AF: 0.177 AC: 1869 AN: 10578

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6935 AN: 68018

Other (OTH) AF: 0.0952 AC: 201 AN: 2112

Alfa AF: 0.0879 Hom.: 75

Bravo AF: 0.0853

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.030
DANN	Benign	0.73
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs13278851; hg19: chr8-9750872;