rs482700

Variant names:

• chr4-115146334-G-A
• rs482700

Your query was ambiguous. Multiple possible variants found:

• chr4-115146334-G-A
• chr4-115146334-G-C
• chr4-115146334-G-T

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 0.773 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.905 AC: 37588 AN: 41536

American (AMR) AF: 0.738 AC: 11286 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2017 AN: 3472

East Asian (EAS) AF: 0.663 AC: 3425 AN: 5168

South Asian (SAS) AF: 0.575 AC: 2768 AN: 4818

European-Finnish (FIN) AF: 0.810 AC: 8573 AN: 10590

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.727 AC: 49436 AN: 67988

Other (OTH) AF: 0.749 AC: 1583 AN: 2114

Alfa AF: 0.725 Hom.: 20630

Bravo AF: 0.780

Asia WGS AF: 0.633 AC: 2196 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs482700; hg19: chr4-116067490;