rs4530903

Variant names:

• chr6-32614112-C-T
• rs4530903

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 0.0989 in 152,048 control chromosomes in the GnomAD database, including 895 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 0.099 (895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0989 AC: 15027 AN: 151930 Hom.: 895 Cov.: 32

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.0931

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0989 AC: 15037 AN: 152048 Hom.: 895 Cov.: 32 AF XY: 0.100 AC XY: 7466 AN XY: 74298

Gnomad4 AFR AF: 0.0689

Gnomad4 AMR AF: 0.0929

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0378

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.100

Alfa AF: 0.105 Hom.: 574

Bravo AF: 0.0901

Asia WGS AF: 0.0360 AC: 124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4530903; hg19: chr6-32581889;