chr4-122058484-A-G

Variant names:

• chr4-122058484-A-G
• rs12510683

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 0.205 in 152,088 control chromosomes in the GnomAD database, including 4,602 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 0.21 (4602 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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: 0.205 AC: 31207 AN: 151970 Hom.: 4584 Cov.: 31

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.205 AC: 31241 AN: 152088 Hom.: 4602 Cov.: 31 AF XY: 0.209 AC XY: 15513 AN XY: 74338

African (AFR) AF: 0.0528 AC: 2191 AN: 41506

American (AMR) AF: 0.436 AC: 6660 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2594 AN: 5156

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4824

European-Finnish (FIN) AF: 0.151 AC: 1595 AN: 10568

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15283 AN: 67976

Other (OTH) AF: 0.234 AC: 493 AN: 2110

Alfa AF: 0.211 Hom.: 929

Bravo AF: 0.227

Asia WGS AF: 0.327 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.84
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs12510683; hg19: chr4-122979639;