rs1531732

Variant names:

• chr3-99355841-A-G
• rs1531732
• ENST00000715235.1:n.51+24389A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000715235.1(ENSG00000243296):​n.51+24389A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,230 control chromosomes in the GnomAD database, including 2,698 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 0.13 (2698 hom., cov: 32)
• Consequence: ENSG00000243296 ENST00000715235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 0 publications found

Genes affected

ENSG00000243296 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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
ENSG00000243296	ENST00000715235.1	n.51+24389A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19316 AN: 152112 Hom.: 2685 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.127 AC: 19377 AN: 152230 Hom.: 2698 Cov.: 32 AF XY: 0.127 AC XY: 9476 AN XY: 74424

African (AFR) AF: 0.336 AC: 13928 AN: 41510

American (AMR) AF: 0.0698 AC: 1067 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0328 AC: 114 AN: 3472

East Asian (EAS) AF: 0.271 AC: 1402 AN: 5164

South Asian (SAS) AF: 0.124 AC: 598 AN: 4830

European-Finnish (FIN) AF: 0.0305 AC: 324 AN: 10620

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0241 AC: 1637 AN: 68022

Other (OTH) AF: 0.125 AC: 264 AN: 2114

Alfa AF: 0.0782 Hom.: 232

Bravo AF: 0.138

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.54
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1531732; hg19: chr3-99074685;