XM_024450773.2:c.4810-133685G>A

Variant names:

• chr17-46915371-G-A
• rs1662594
• XM_024450773.2:c.4810-133685G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_024450773.2(LRRC37A2):​c.4810-133685G>A variant causes a intron 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: LRRC37A2 XM_024450773.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 11 publications found

Genes affected

LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000297729 (HGNC:):

GOSR2-DT (HGNC:55346): (GOSR2 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750540.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297729	ENST00000750540.1		n.322G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000297729	ENST00000750541.1		n.359G>A		non_coding_transcript_exon	Exon 2 of 2
	GOSR2-DT	ENST00000715847.1		n.270-5205C>T		intron	N/A

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

African (AFR) AF: 0.321 AC: 13319 AN: 41452

American (AMR) AF: 0.416 AC: 6363 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2303 AN: 5156

South Asian (SAS) AF: 0.479 AC: 2300 AN: 4800

European-Finnish (FIN) AF: 0.410 AC: 4333 AN: 10556

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25866 AN: 67962

Other (OTH) AF: 0.385 AC: 812 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1662594; hg19: chr17-44992737;