8-115062231-T-C

Variant names:

• chr8-115062231-T-C
• rs1898280

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 0.429 in 151,946 control chromosomes in the GnomAD database, including 18,106 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 0.43 (18106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 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: 0.428 AC: 64990 AN: 151826 Hom.: 18052 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.429 AC: 65110 AN: 151946 Hom.: 18106 Cov.: 32 AF XY: 0.431 AC XY: 32012 AN XY: 74280

African (AFR) AF: 0.748 AC: 31013 AN: 41438

American (AMR) AF: 0.447 AC: 6824 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3472

East Asian (EAS) AF: 0.809 AC: 4175 AN: 5162

South Asian (SAS) AF: 0.480 AC: 2312 AN: 4818

European-Finnish (FIN) AF: 0.227 AC: 2400 AN: 10554

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16239 AN: 67926

Other (OTH) AF: 0.388 AC: 820 AN: 2114

Alfa AF: 0.237 Hom.: 8848

Bravo AF: 0.462

Asia WGS AF: 0.644 AC: 2231 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.46
DANN	Benign	0.63
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1898280; hg19: chr8-116074460;