chr8-87856112-C-A

Variant names:

• chr8-87856112-C-A
• rs12543318

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 0.673 in 152,088 control chromosomes in the GnomAD database, including 35,332 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 0.67 (35332 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 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: 0.673 AC: 102295 AN: 151966 Hom.: 35290 Cov.: 33

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.673 AC: 102395 AN: 152088 Hom.: 35332 Cov.: 33 AF XY: 0.667 AC XY: 49556 AN XY: 74334

African (AFR) AF: 0.793 AC: 32913 AN: 41496

American (AMR) AF: 0.565 AC: 8643 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2116 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2142 AN: 5164

South Asian (SAS) AF: 0.529 AC: 2555 AN: 4826

European-Finnish (FIN) AF: 0.654 AC: 6910 AN: 10566

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.661 AC: 44922 AN: 67964

Other (OTH) AF: 0.630 AC: 1331 AN: 2114

Alfa AF: 0.661 Hom.: 102377

Bravo AF: 0.668

Asia WGS AF: 0.538 AC: 1875 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	16
DANN	Benign	0.45
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs12543318; hg19: chr8-88868340;