chr8-2363464-T-C

Variant names:

• chr8-2363464-T-C
• rs4876153

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 0.271 in 152,150 control chromosomes in the GnomAD database, including 6,835 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 0.27 (6835 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 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: 0.271 AC: 41273 AN: 152032 Hom.: 6839 Cov.: 33

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.271 AC: 41271 AN: 152150 Hom.: 6835 Cov.: 33 AF XY: 0.281 AC XY: 20885 AN XY: 74378

African (AFR) AF: 0.0859 AC: 3569 AN: 41538

American (AMR) AF: 0.345 AC: 5274 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2140 AN: 5166

South Asian (SAS) AF: 0.381 AC: 1838 AN: 4822

European-Finnish (FIN) AF: 0.424 AC: 4482 AN: 10570

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21600 AN: 67982

Other (OTH) AF: 0.287 AC: 606 AN: 2112

Alfa AF: 0.306 Hom.: 27645

Bravo AF: 0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs4876153; hg19: chr8-2304334;