rs815703

Variant names:

• chr3-61287099-T-A
• rs815703
• ENST00000809925.1:n.52-11391T>A

Variant summary

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

The ENST00000809925.1(ENSG00000305269):​n.52-11391T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,154 control chromosomes in the GnomAD database, including 1,783 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 0.15 (1783 hom., cov: 32)
• Consequence: ENSG00000305269 ENST00000809925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 1 publications found

Genes affected

ENSG00000305269 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377114	XR_001740725.2	n.708-2435A>T		intron_variant	Intron 5 of 5
LOC105377114	XR_940892.3	n.822-2435A>T		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305269	ENST00000809925.1	n.52-11391T>A		intron_variant	Intron 1 of 3
ENSG00000305269	ENST00000809926.1	n.55-24868T>A		intron_variant	Intron 1 of 2
ENSG00000305269	ENST00000809927.1	n.255+15044T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22685 AN: 152036 Hom.: 1781 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.149 AC: 22694 AN: 152154 Hom.: 1783 Cov.: 32 AF XY: 0.149 AC XY: 11078 AN XY: 74380

African (AFR) AF: 0.142 AC: 5877 AN: 41510

American (AMR) AF: 0.158 AC: 2415 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3468

East Asian (EAS) AF: 0.0651 AC: 337 AN: 5174

South Asian (SAS) AF: 0.101 AC: 488 AN: 4828

European-Finnish (FIN) AF: 0.162 AC: 1717 AN: 10584

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10813 AN: 67980

Other (OTH) AF: 0.157 AC: 332 AN: 2116

Alfa AF: 0.157 Hom.: 239

Bravo AF: 0.151

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs815703; hg19: chr3-61272773;