rs1530320

Variant names:

• chr4-99445484-T-C
• rs1530320

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 0.143 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.197 AC: 8151 AN: 41442

American (AMR) AF: 0.0946 AC: 1440 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3466

East Asian (EAS) AF: 0.0856 AC: 443 AN: 5176

South Asian (SAS) AF: 0.159 AC: 764 AN: 4814

European-Finnish (FIN) AF: 0.154 AC: 1626 AN: 10576

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8404 AN: 67934

Other (OTH) AF: 0.124 AC: 262 AN: 2114

Alfa AF: 0.135 Hom.: 530

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
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs1530320; hg19: chr4-100366641;