chr8-109153787-C-G

Variant names:

• chr8-109153787-C-G
• rs4314624

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 0.414 in 151,976 control chromosomes in the GnomAD database, including 13,627 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 0.41 (13627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 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: 0.413 AC: 62775 AN: 151856 Hom.: 13597 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.414 AC: 62864 AN: 151976 Hom.: 13627 Cov.: 32 AF XY: 0.418 AC XY: 31078 AN XY: 74282

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.377

Alfa AF: 0.387 Hom.: 1518

Bravo AF: 0.424

Asia WGS AF: 0.527 AC: 1831 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	0.37
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4314624; hg19: chr8-110166016;