chr8-55687218-G-A

Variant names:

• chr8-55687218-G-A
• rs4738393

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 0.306 in 152,010 control chromosomes in the GnomAD database, including 7,312 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 0.31 (7312 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 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: 0.307 AC: 46562 AN: 151892 Hom.: 7310 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.306 AC: 46566 AN: 152010 Hom.: 7312 Cov.: 31 AF XY: 0.311 AC XY: 23120 AN XY: 74306

African (AFR) AF: 0.288 AC: 11950 AN: 41482

American (AMR) AF: 0.323 AC: 4935 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 823 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2528 AN: 5146

South Asian (SAS) AF: 0.450 AC: 2163 AN: 4810

European-Finnish (FIN) AF: 0.298 AC: 3150 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20039 AN: 67940

Other (OTH) AF: 0.317 AC: 669 AN: 2108

Alfa AF: 0.302 Hom.: 10978

Bravo AF: 0.305

Asia WGS AF: 0.446 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.78
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs4738393; hg19: chr8-56599777;