rs6552429

Variant names:

• chr4-180572024-G-C
• rs6552429

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 0.664 in 152,128 control chromosomes in the GnomAD database, including 34,334 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 0.66 (34334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.732 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: 0.664 AC: 100902 AN: 152010 Hom.: 34324 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.664 AC: 100956 AN: 152128 Hom.: 34334 Cov.: 32 AF XY: 0.663 AC XY: 49294 AN XY: 74374

African (AFR) AF: 0.538 AC: 22326 AN: 41466

American (AMR) AF: 0.688 AC: 10521 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2382 AN: 3472

East Asian (EAS) AF: 0.409 AC: 2116 AN: 5176

South Asian (SAS) AF: 0.585 AC: 2820 AN: 4822

European-Finnish (FIN) AF: 0.807 AC: 8545 AN: 10594

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50136 AN: 68002

Other (OTH) AF: 0.673 AC: 1421 AN: 2112

Alfa AF: 0.701 Hom.: 4660

Bravo AF: 0.652

Asia WGS AF: 0.537 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.20
DANN	Benign	0.44
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs6552429; hg19: chr4-181493177;