rs1530320

Variant names:

• chr4-99445484-T-C
• rs1530320

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 0.143 in 151,958 control chromosomes in the GnomAD database, including 1,741 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 0.14 (1741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

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 (AFR) allele frequency at 95% confidence interval = 0.193 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: 0.143 AC: 21642 AN: 151840 Hom.: 1739 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0947

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.143 AC: 21660 AN: 151958 Hom.: 1741 Cov.: 32 AF XY: 0.144 AC XY: 10681 AN XY: 74286

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.0946

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0856

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.124

Alfa AF: 0.137 Hom.: 345

Bravo AF: 0.137

Asia WGS AF: 0.121 AC: 421 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	3.7
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1530320; hg19: chr4-100366641;