rs4242384

chr8-127506309-C-Achr8-127506309-C-G

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 0.882 in 151,038 control chromosomes in the GnomAD database, including 58,859 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 0.88 (58859 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.906 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: 0.882 AC: 133159 AN: 150920 Hom.: 58816 Cov.: 25

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.882 AC: 133259 AN: 151038 Hom.: 58859 Cov.: 25 AF XY: 0.881 AC XY: 64851 AN XY: 73620

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.919

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.897

Alfa AF: 0.897 Hom.: 106257

Bravo AF: 0.884

Asia WGS AF: 0.820 AC: 2856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.40
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4242384; hg19: chr8-128518554;