rs6531193

chr2-19689466-C-T

Variant summary

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

The XR_007086240.1(LOC124905977):n.392+15307G>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 0.443 in 151,982 control chromosomes in the GnomAD database, including 15,640 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 0.44 (15640 hom., cov: 31)
• Consequence: LOC124905977 XR_007086240.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

LOC124905977 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905977	XR_007086240.1	n.392+15307G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67272 AN: 151862 Hom.: 15637 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.443 AC: 67295 AN: 151982 Hom.: 15640 Cov.: 31 AF XY: 0.436 AC XY: 32392 AN XY: 74306

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.0729

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.464

Alfa AF: 0.486 Hom.: 9509

Bravo AF: 0.438

Asia WGS AF: 0.256 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6531193; hg19: chr2-19889227;