rs1662594

chr17-46915371-G-A

Variant summary

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

The XR_002958114.2(LOC112268191):n.389G>A 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 0.374 in 151,986 control chromosomes in the GnomAD database, including 10,717 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 0.37 (10717 hom., cov: 31)
• Consequence: LOC112268191 XR_002958114.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938

Genes affected

LOC112268191 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268191	XR_002958114.2	n.389G>A		non_coding_transcript_exon_variant	2/2
LRRC37A2	XM_024450773.2	c.4810-133685G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56871 AN: 151870 Hom.: 10716 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.374 AC: 56898 AN: 151986 Hom.: 10717 Cov.: 31 AF XY: 0.378 AC XY: 28079 AN XY: 74256

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.385

Alfa AF: 0.376 Hom.: 3496

Bravo AF: 0.370

Asia WGS AF: 0.441 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.6
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1662594; hg19: chr17-44992737;