rs4319530

Variant names:

• chr11-58632356-A-G
• rs4319530

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 0.441 in 151,992 control chromosomes in the GnomAD database, including 15,071 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 0.44 (15071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 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: 0.441 AC: 67001 AN: 151872 Hom.: 15043 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.441 AC: 67073 AN: 151992 Hom.: 15071 Cov.: 32 AF XY: 0.444 AC XY: 33005 AN XY: 74296

African (AFR) AF: 0.508 AC: 21057 AN: 41436

American (AMR) AF: 0.409 AC: 6255 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1359 AN: 3466

East Asian (EAS) AF: 0.321 AC: 1656 AN: 5166

South Asian (SAS) AF: 0.457 AC: 2204 AN: 4820

European-Finnish (FIN) AF: 0.499 AC: 5258 AN: 10546

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27824 AN: 67958

Other (OTH) AF: 0.429 AC: 906 AN: 2112

Alfa AF: 0.438 Hom.: 1950

Bravo AF: 0.435

Asia WGS AF: 0.396 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.50
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs4319530; hg19: chr11-58399829;