rs12700524

chr7-24281795-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745132.2(LOC107986777):n.209+37562T>C variant causes a intron, non coding transcript 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: LOC107986777 XR_001745132.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

LOC107986777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.209+37562T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.0746

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.126

Alfa AF: 0.138 Hom.: 804

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12700524; hg19: chr7-24321414;