rs4452638

Variant names:

• chr6-27261486-G-A
• rs4452638

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 0.0825 in 150,020 control chromosomes in the GnomAD database, including 606 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 0.082 (606 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 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: 0.0825 AC: 12365 AN: 149922 Hom.: 606 Cov.: 31

Gnomad AFR AF: 0.0707

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0473

Gnomad ASJ AF: 0.0465

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0191

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0659

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

GnomAD4 genome AF: 0.0825 AC: 12370 AN: 150020 Hom.: 606 Cov.: 31 AF XY: 0.0776 AC XY: 5672 AN XY: 73110

Gnomad4 AFR AF: 0.0708

Gnomad4 AMR AF: 0.0472

Gnomad4 ASJ AF: 0.0465

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0187

Gnomad4 FIN AF: 0.0546

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0647

Alfa AF: 0.0999 Hom.: 846

Bravo AF: 0.0820

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4452638; hg19: chr6-27229265;