XM_024450773.2:c.4810-135900A>G

Variant names:

• chr17-46913156-A-G
• rs197915
• XM_024450773.2:c.4810-135900A>G

Variant summary

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

The XM_024450773.2(LRRC37A2):​c.4810-135900A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,176 control chromosomes in the GnomAD database, including 11,508 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 0.39 (11508 hom., cov: 32)
• Consequence: LRRC37A2 XM_024450773.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 7 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]

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

ENSG00000297729 (HGNC:):

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 = 0.465 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715847.1. 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
	GOSR2-DT	ENST00000715847.1		n.270-2990T>C		intron	N/A
	ENSG00000297729	ENST00000750540.1		n.101+201A>G		intron	N/A
	ENSG00000297729	ENST00000750541.1		n.99+201A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58796 AN: 152058 Hom.: 11501 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.387 AC: 58832 AN: 152176 Hom.: 11508 Cov.: 32 AF XY: 0.391 AC XY: 29066 AN XY: 74372

African (AFR) AF: 0.322 AC: 13382 AN: 41516

American (AMR) AF: 0.428 AC: 6543 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2173 AN: 5180

South Asian (SAS) AF: 0.481 AC: 2318 AN: 4820

European-Finnish (FIN) AF: 0.426 AC: 4510 AN: 10576

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27264 AN: 68004

Other (OTH) AF: 0.408 AC: 860 AN: 2108

Alfa AF: 0.391 Hom.: 3236

Bravo AF: 0.380

Asia WGS AF: 0.431 AC: 1502 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	0.21
DANN	Benign	0.20
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs197915; hg19: chr17-44990522;