rs4556079

Variant names:

• chr8-139220692-T-C
• rs4556079

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 0.239 in 152,142 control chromosomes in the GnomAD database, including 4,916 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 0.24 (4916 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.369 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: 0.239 AC: 36353 AN: 152026 Hom.: 4907 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.239 AC: 36378 AN: 152142 Hom.: 4916 Cov.: 33 AF XY: 0.243 AC XY: 18051 AN XY: 74370

African (AFR) AF: 0.124 AC: 5133 AN: 41552

American (AMR) AF: 0.377 AC: 5762 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 817 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1117 AN: 5174

South Asian (SAS) AF: 0.141 AC: 682 AN: 4828

European-Finnish (FIN) AF: 0.309 AC: 3267 AN: 10562

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.277 AC: 18851 AN: 67956

Other (OTH) AF: 0.227 AC: 478 AN: 2110

Alfa AF: 0.266 Hom.: 14396

Bravo AF: 0.242

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.6
DANN	Benign	0.89
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs4556079; hg19: chr8-140232935;