rs2587988

Positions:

• chr3-130201415-C-T

Variant summary

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

The XR_007096085.1(LOC124909433):​n.175C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,122 control chromosomes in the GnomAD database, including 6,803 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 (6803 hom., cov: 32)
• Consequence: LOC124909433 XR_007096085.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

Genes affected

LOC124909433 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124909433	XR_007096085.1	n.175C>T		non_coding_transcript_exon_variant	2/2
		n.130201415C>T		intergenic_region
LOC107986133	XR_001740907.2	n.3382+534G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42545 AN: 152004 Hom.: 6792 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.280 AC: 42570 AN: 152122 Hom.: 6803 Cov.: 32 AF XY: 0.286 AC XY: 21240 AN XY: 74346

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.286

Alfa AF: 0.308 Hom.: 15267

Bravo AF: 0.285

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2587988; hg19: chr3-129920258;