rs197915

Positions:

• chr17-46913156-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(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 = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC37A2	XM_024450773.2	c.4810-135900A>G		intron_variant			XP_024306541.1
		n.46913156A>G		intergenic_region
LOC112268191	XR_002958114.2	n.129+201A>G		intron_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.408

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs197915; hg19: chr17-44990522;