rs1530320

Positions:

• chr4-99445484-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;