XM_024450773.2:c.4810-136534T>A

Variant names:

• chr17-46912522-T-A
• rs197912
• XM_024450773.2:c.4810-136534T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_024450773.2(LRRC37A2):​c.4810-136534T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,044 control chromosomes in the GnomAD database, including 10,558 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 (10558 hom., cov: 32)
• Consequence: LRRC37A2 XM_024450773.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 8 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)

LINC01974 (HGNC:52801): (long intergenic non-protein coding RNA 1974)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750347.1. 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
	LINC01974	NR_184095.1		n.280A>T		non_coding_transcript_exon	Exon 1 of 3
	LINC01974	NR_184096.1		n.220+60A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOSR2-DT	ENST00000750347.1		n.256A>T		non_coding_transcript_exon	Exon 1 of 3
	GOSR2-DT	ENST00000575126.2	TSL:3	n.220+60A>T		intron	N/A
	GOSR2-DT	ENST00000715847.1		n.270-2356A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56462 AN: 151926 Hom.: 10559 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.372 AC: 56489 AN: 152044 Hom.: 10558 Cov.: 32 AF XY: 0.375 AC XY: 27901 AN XY: 74308

African (AFR) AF: 0.360 AC: 14932 AN: 41476

American (AMR) AF: 0.398 AC: 6088 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1000 AN: 3466

East Asian (EAS) AF: 0.432 AC: 2222 AN: 5148

South Asian (SAS) AF: 0.470 AC: 2266 AN: 4820

European-Finnish (FIN) AF: 0.396 AC: 4179 AN: 10566

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24454 AN: 67964

Other (OTH) AF: 0.378 AC: 797 AN: 2110

Alfa AF: 0.356 Hom.: 1228

Bravo AF: 0.367

Asia WGS AF: 0.433 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	16
DANN	Benign	0.77
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs197912; hg19: chr17-44989888;