rs4530903

Variant names:

• chr6-32614112-C-T
• rs4530903

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 0.0989 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
• Publications: 59 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0689 AC: 2859 AN: 41506

American (AMR) AF: 0.0929 AC: 1419 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 452 AN: 3472

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5168

South Asian (SAS) AF: 0.0378 AC: 182 AN: 4814

European-Finnish (FIN) AF: 0.201 AC: 2115 AN: 10530

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7497 AN: 67976

Other (OTH) AF: 0.100 AC: 211 AN: 2108

Alfa AF: 0.0982 Hom.: 2229

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4530903; hg19: chr6-32581889;