rs7725288

chr5-36328204-C-A

Variant summary

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

The XR_007058733.1(LOC124900962):n.299+389C>A 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 0.577 in 152,078 control chromosomes in the GnomAD database, including 26,724 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 0.58 (26724 hom., cov: 33)
• Consequence: LOC124900962 XR_007058733.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

Genes affected

LOC124900962 (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 = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900962	XR_007058733.1	n.299+389C>A		intron_variant, non_coding_transcript_variant
LOC124900962	XR_007058732.1	n.943+389C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87707 AN: 151960 Hom.: 26681 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.577 AC: 87799 AN: 152078 Hom.: 26724 Cov.: 33 AF XY: 0.571 AC XY: 42448 AN XY: 74316

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.537

Alfa AF: 0.525 Hom.: 11262

Bravo AF: 0.577

Asia WGS AF: 0.373 AC: 1296 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	9.3
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7725288; hg19: chr5-36328306;