rs4689388

Variant names:

• chr4-6268329-G-A
• rs4689388

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 0.646 in 152,038 control chromosomes in the GnomAD database, including 32,479 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 0.65 (32479 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 68 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 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: 0.646 AC: 98145 AN: 151920 Hom.: 32436 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.646 AC: 98243 AN: 152038 Hom.: 32479 Cov.: 33 AF XY: 0.648 AC XY: 48195 AN XY: 74320

African (AFR) AF: 0.711 AC: 29476 AN: 41442

American (AMR) AF: 0.691 AC: 10555 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2323 AN: 3470

East Asian (EAS) AF: 0.943 AC: 4889 AN: 5184

South Asian (SAS) AF: 0.711 AC: 3424 AN: 4818

European-Finnish (FIN) AF: 0.549 AC: 5793 AN: 10552

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39796 AN: 67972

Other (OTH) AF: 0.654 AC: 1381 AN: 2112

Alfa AF: 0.615 Hom.: 88750

Bravo AF: 0.659

Asia WGS AF: 0.829 AC: 2884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.33
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4689388; hg19: chr4-6270056;