rs10491148

chr17-46913279-C-T

Variant summary

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

The XR_002958114.2(LOC112268191):n.129+324C>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 0.0337 in 152,330 control chromosomes in the GnomAD database, including 165 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 0.034 (165 hom., cov: 32)
• Consequence: LOC112268191 XR_002958114.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

LOC112268191 (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 (AFR) allele frequency at 95% confidence interval = 0.0804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268191	XR_002958114.2	n.129+324C>T		intron_variant, non_coding_transcript_variant
LRRC37A2	XM_024450773.2	c.4810-135777C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0337 AC: 5125 AN: 152212 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0220

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00310

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0139

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0337 AC: 5126 AN: 152330 Hom.: 165 Cov.: 32 AF XY: 0.0327 AC XY: 2433 AN XY: 74492

Gnomad4 AFR AF: 0.0828

Gnomad4 AMR AF: 0.0220

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.00290

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.0139

Gnomad4 OTH AF: 0.0359

Alfa AF: 0.0241 Hom.: 13

Bravo AF: 0.0371

Asia WGS AF: 0.00577 AC: 20 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	1.9
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491148; hg19: chr17-44990645;