rs4512366

Variant names:

• chr8-124447478-G-A
• rs4512366

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 0.167 in 152,162 control chromosomes in the GnomAD database, including 2,455 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 0.17 (2455 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 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: 0.168 AC: 25473 AN: 152044 Hom.: 2452 Cov.: 32

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0889

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.167 AC: 25479 AN: 152162 Hom.: 2455 Cov.: 32 AF XY: 0.163 AC XY: 12095 AN XY: 74376

African (AFR) AF: 0.0828 AC: 3439 AN: 41522

American (AMR) AF: 0.254 AC: 3873 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3472

East Asian (EAS) AF: 0.0893 AC: 462 AN: 5176

South Asian (SAS) AF: 0.0947 AC: 457 AN: 4824

European-Finnish (FIN) AF: 0.166 AC: 1755 AN: 10580

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14229 AN: 68010

Other (OTH) AF: 0.196 AC: 413 AN: 2112

Alfa AF: 0.207 Hom.: 5947

Bravo AF: 0.177

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.72
DANN	Benign	0.27
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4512366; hg19: chr8-125459719;