4-116570472-A-G

Variant names:

• chr4-116570472-A-G
• rs1425629

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 0.668 in 151,938 control chromosomes in the GnomAD database, including 34,389 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 0.67 (34389 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.751 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: 0.668 AC: 101470 AN: 151820 Hom.: 34355 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.668 AC: 101568 AN: 151938 Hom.: 34389 Cov.: 31 AF XY: 0.672 AC XY: 49884 AN XY: 74248

African (AFR) AF: 0.733 AC: 30362 AN: 41426

American (AMR) AF: 0.762 AC: 11625 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2806 AN: 3468

East Asian (EAS) AF: 0.575 AC: 2965 AN: 5160

South Asian (SAS) AF: 0.688 AC: 3321 AN: 4824

European-Finnish (FIN) AF: 0.604 AC: 6382 AN: 10566

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41891 AN: 67930

Other (OTH) AF: 0.704 AC: 1487 AN: 2112

Alfa AF: 0.656 Hom.: 4890

Bravo AF: 0.682

Asia WGS AF: 0.642 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.35
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1425629; hg19: chr4-117491628;