rs12700524

Variant names:

• chr7-24281795-A-G
• rs12700524
• ENST00000718234.1:n.319+37562T>C

Variant summary

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

The ENST00000718234.1(ENSG00000228944):​n.319+37562T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,264 control chromosomes in the GnomAD database, including 1,201 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 0.12 (1201 hom., cov: 32)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 8 publications found

Genes affected

ENSG00000228944 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.209+37562T>C		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-84766T>C		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.209+37562T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228944	ENST00000718234.1	n.319+37562T>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745512.1	n.341+37562T>C		intron_variant	Intron 2 of 5
ENSG00000228944	ENST00000745513.1	n.309+37562T>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745514.1	n.329-11965T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18691 AN: 152146 Hom.: 1201 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.123 AC: 18702 AN: 152264 Hom.: 1201 Cov.: 32 AF XY: 0.120 AC XY: 8923 AN XY: 74456

African (AFR) AF: 0.109 AC: 4539 AN: 41556

American (AMR) AF: 0.104 AC: 1595 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3472

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5186

South Asian (SAS) AF: 0.0746 AC: 360 AN: 4828

European-Finnish (FIN) AF: 0.117 AC: 1237 AN: 10600

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

European-Non Finnish (NFE) AF: 0.147 AC: 9963 AN: 68006

Other (OTH) AF: 0.126 AC: 267 AN: 2114

Alfa AF: 0.136 Hom.: 1117

Bravo AF: 0.123

Asia WGS AF: 0.0640 AC: 225 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	0.0090
DANN	Benign	0.49
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12700524; hg19: chr7-24321414;