rs12440824

Variant names:

• chr15-47932774-A-G
• rs12440824
• ENST00000560900.1:n.195+48270A>G

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.195+48270A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,178 control chromosomes in the GnomAD database, including 2,853 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 0.18 (2853 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 1 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.142+48270A>G		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.142+48270A>G		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.82+17412A>G		intron_variant	Intron 1 of 2
LOC124900354	XR_007064618.1	n.143-16582A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.195+48270A>G		intron_variant	Intron 1 of 2	4
ENSG00000259754	ENST00000662551.1	n.189-59935A>G		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.189-59935A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26880 AN: 152060 Hom.: 2848 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.177 AC: 26916 AN: 152178 Hom.: 2853 Cov.: 32 AF XY: 0.178 AC XY: 13262 AN XY: 74414

African (AFR) AF: 0.270 AC: 11194 AN: 41502

American (AMR) AF: 0.222 AC: 3392 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1710 AN: 5160

South Asian (SAS) AF: 0.181 AC: 875 AN: 4822

European-Finnish (FIN) AF: 0.124 AC: 1313 AN: 10598

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.112 AC: 7648 AN: 68014

Other (OTH) AF: 0.170 AC: 359 AN: 2110

Alfa AF: 0.136 Hom.: 2216

Bravo AF: 0.188

Asia WGS AF: 0.292 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.76
DANN	Benign	0.92
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12440824; hg19: chr15-48224971;