rs7712169

chr5-12383830-G-A

Variant summary

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

The XR_925792.3(LOC105374655):n.523-15836C>T 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 0.0575 in 152,092 control chromosomes in the GnomAD database, including 528 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 0.058 (528 hom., cov: 32)
• Consequence: LOC105374655 XR_925792.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611

Genes affected

LOC105374655 (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 (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374655	XR_925792.3	n.523-15836C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 8737 AN: 151972 Hom.: 526 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0522

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

GnomAD4 genome AF: 0.0575 AC: 8750 AN: 152092 Hom.: 528 Cov.: 32 AF XY: 0.0568 AC XY: 4225 AN XY: 74338

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0328

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0780

Gnomad4 FIN AF: 0.0136

Gnomad4 NFE AF: 0.0187

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0311 Hom.: 113

Bravo AF: 0.0614

Asia WGS AF: 0.0390 AC: 134 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	0.21
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7712169; hg19: chr5-12383942;