rs197932

Variant names:

• chr17-46896981-T-C
• rs197932
• XM_024450773.2:c.4810-152075T>C

Variant summary

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

The XM_024450773.2(LRRC37A2):​c.4810-152075T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,074 control chromosomes in the GnomAD database, including 21,247 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 0.48 (21247 hom., cov: 32)
• Consequence: LRRC37A2 XM_024450773.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72877 AN: 151956 Hom.: 21193 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.480 AC: 72986 AN: 152074 Hom.: 21247 Cov.: 32 AF XY: 0.476 AC XY: 35403 AN XY: 74346

African (AFR) AF: 0.828 AC: 34368 AN: 41500

American (AMR) AF: 0.441 AC: 6728 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3466

East Asian (EAS) AF: 0.290 AC: 1500 AN: 5166

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4818

European-Finnish (FIN) AF: 0.335 AC: 3549 AN: 10582

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22478 AN: 67950

Other (OTH) AF: 0.450 AC: 953 AN: 2116

Alfa AF: 0.372 Hom.: 22594

Bravo AF: 0.503

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.067
DANN	Benign	0.23
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs197932; hg19: chr17-44974347;