rs754524

Positions:

• chr2-21088669-T-G

Variant summary

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

The XR_007088660.1(LOC124905593):​n.579-7452T>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 0.193 in 152,230 control chromosomes in the GnomAD database, including 3,476 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 0.19 (3476 hom., cov: 32)
• Consequence: LOC124905593 XR_007088660.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768

Genes affected

LOC124905593 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905593	XR_007088660.1	n.579-7452T>G		intron_variant, non_coding_transcript_variant
LOC124905593	XR_007088659.1	n.579-7452T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29422 AN: 152112 Hom.: 3474 Cov.: 32

Gnomad AFR AF: 0.0573

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.193 AC: 29430 AN: 152230 Hom.: 3476 Cov.: 32 AF XY: 0.192 AC XY: 14324 AN XY: 74440

Gnomad4 AFR AF: 0.0572

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.178

Alfa AF: 0.240 Hom.: 2646

Bravo AF: 0.190

Asia WGS AF: 0.132 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754524; hg19: chr2-21311541;