rs754523

chr2-21088819-A-G

Variant summary

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

The XR_007088660.1(LOC124905593):n.579-7302A>G 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 0.278 in 152,130 control chromosomes in the GnomAD database, including 6,081 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 0.28 (6081 hom., cov: 32)
• Consequence: LOC124905593 XR_007088660.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

Genes affected

LOC124905593 (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 (AMR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905593	XR_007088660.1	n.579-7302A>G		intron_variant, non_coding_transcript_variant
LOC124905593	XR_007088659.1	n.579-7302A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42326 AN: 152012 Hom.: 6083 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.278 AC: 42340 AN: 152130 Hom.: 6081 Cov.: 32 AF XY: 0.276 AC XY: 20484 AN XY: 74338

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.263

Alfa AF: 0.294 Hom.: 3485

Bravo AF: 0.283

Asia WGS AF: 0.203 AC: 706 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	1.8
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754523; hg19: chr2-21311691;