rs4628236

chr8-109159916-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.347 in 151,936 control chromosomes in the GnomAD database, including 9,513 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 0.35 (9513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52730 AN: 151818 Hom.: 9504 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.347 AC: 52777 AN: 151936 Hom.: 9513 Cov.: 32 AF XY: 0.352 AC XY: 26118 AN XY: 74234

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.333

Alfa AF: 0.352 Hom.: 1887

Bravo AF: 0.348

Asia WGS AF: 0.476 AC: 1656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.4
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4628236; hg19: chr8-110172145;