rs12524487

chr6-31386461-C-T

Variant summary

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

The XR_007059542.1(LOC124901300):n.75-802C>T 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 0.0616 in 152,210 control chromosomes in the GnomAD database, including 457 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 0.062 (457 hom., cov: 32)
• Consequence: LOC124901300 XR_007059542.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

Genes affected

LOC124901300 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901300	XR_007059542.1	n.75-802C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0617 AC: 9378 AN: 152092 Hom.: 457 Cov.: 32

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.0844

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0616 AC: 9374 AN: 152210 Hom.: 457 Cov.: 32 AF XY: 0.0653 AC XY: 4862 AN XY: 74408

Gnomad4 AFR AF: 0.0135

Gnomad4 AMR AF: 0.0504

Gnomad4 ASJ AF: 0.0629

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.0842

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.0511

Alfa AF: 0.0705 Hom.: 180

Bravo AF: 0.0548

Asia WGS AF: 0.0910 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.1
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12524487; hg19: chr6-31354238;