rs7727533

Variant names:

• chr5-26564434-A-G
• rs7727533

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 0.0433 in 152,248 control chromosomes in the GnomAD database, including 250 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 0.043 (250 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 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: 0.0434 AC: 6597 AN: 152132 Hom.: 253 Cov.: 31

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0433 AC: 6591 AN: 152248 Hom.: 250 Cov.: 31 AF XY: 0.0440 AC XY: 3274 AN XY: 74436

Gnomad4 AFR AF: 0.0701

Gnomad4 AMR AF: 0.0641

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0892

Gnomad4 FIN AF: 0.00989

Gnomad4 NFE AF: 0.0180

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0266 Hom.: 18

Bravo AF: 0.0492

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7727533; hg19: chr5-26564543;