chr5-117642122-G-A

Variant names:

• chr5-117642122-G-A
• rs430952

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 0.408 in 151,982 control chromosomes in the GnomAD database, including 14,435 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 (14435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61890 AN: 151864 Hom.: 14428 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.408 AC: 61933 AN: 151982 Hom.: 14435 Cov.: 32 AF XY: 0.403 AC XY: 29930 AN XY: 74274

African (AFR) AF: 0.634 AC: 26278 AN: 41466

American (AMR) AF: 0.292 AC: 4455 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1239 AN: 3470

East Asian (EAS) AF: 0.0411 AC: 213 AN: 5184

South Asian (SAS) AF: 0.299 AC: 1440 AN: 4820

European-Finnish (FIN) AF: 0.318 AC: 3351 AN: 10526

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.347 AC: 23557 AN: 67944

Other (OTH) AF: 0.411 AC: 869 AN: 2114

Alfa AF: 0.420 Hom.: 1959

Bravo AF: 0.411

Asia WGS AF: 0.213 AC: 741 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.71
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs430952; hg19: chr5-116977817;