4-115146334-G-A

Variant names:

• chr4-115146334-G-A
• rs482700

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 0.773 in 152,174 control chromosomes in the GnomAD database, including 46,202 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 0.77 (46202 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 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: 0.773 AC: 117567 AN: 152056 Hom.: 46158 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.773 AC: 117665 AN: 152174 Hom.: 46202 Cov.: 32 AF XY: 0.772 AC XY: 57457 AN XY: 74394

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.749

Alfa AF: 0.724 Hom.: 18301

Bravo AF: 0.780

Asia WGS AF: 0.633 AC: 2196 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs482700; hg19: chr4-116067490;