chr8-55655090-C-A

Variant names:

• chr8-55655090-C-A
• rs4738382

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 0.342 in 152,008 control chromosomes in the GnomAD database, including 12,240 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 0.34 (12240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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: 0.342 AC: 51921 AN: 151890 Hom.: 12190 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.342 AC: 52021 AN: 152008 Hom.: 12240 Cov.: 32 AF XY: 0.344 AC XY: 25585 AN XY: 74322

African (AFR) AF: 0.670 AC: 27753 AN: 41442

American (AMR) AF: 0.191 AC: 2912 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3472

East Asian (EAS) AF: 0.266 AC: 1374 AN: 5160

South Asian (SAS) AF: 0.389 AC: 1875 AN: 4822

European-Finnish (FIN) AF: 0.240 AC: 2538 AN: 10562

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13910 AN: 67966

Other (OTH) AF: 0.303 AC: 639 AN: 2108

Alfa AF: 0.245 Hom.: 7770

Bravo AF: 0.348

Asia WGS AF: 0.362 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.18
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs4738382; hg19: chr8-56567649;