rs4689388

Variant names:

• chr4-6268329-G-A
• rs4689388

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.646 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

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.654

Alfa AF: 0.612 Hom.: 30764

Bravo AF: 0.659

Asia WGS AF: 0.829 AC: 2884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4689388; hg19: chr4-6270056;