rs11015624

chr10-27249640-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_003525.2(LRRC37A6P):n.2667C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,324,402 control chromosomes in the GnomAD database, including 29,304 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 0.19 (2810 hom., cov: 32)
  • Exomes 𝑓: 0.20 (26494 hom.)
• Consequence: LRRC37A6P NR_003525.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

LRRC37A6P (HGNC:33746): (leucine rich repeat containing 37 member A6, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC37A6P	NR_003525.2	n.2667C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000284414.4	n.923C>T		non_coding_transcript_exon_variant	1/1
LRRC37A6P	ENST00000448648.2	n.2154C>T		non_coding_transcript_exon_variant	1/1
	ENST00000574842.1	n.256-418G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28326 AN: 152000 Hom.: 2803 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.0534

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.170

GnomAD3 exomes AF: 0.177 AC: 44476 AN: 250942 Hom.: 4606 AF XY: 0.169 AC XY: 22906 AN XY: 135684

Gnomad AFR exome AF: 0.193

Gnomad AMR exome AF: 0.258

Gnomad ASJ exome AF: 0.166

Gnomad EAS exome AF: 0.0123

Gnomad SAS exome AF: 0.0575

Gnomad FIN exome AF: 0.208

Gnomad NFE exome AF: 0.205

Gnomad OTH exome AF: 0.180

GnomAD4 exome AF: 0.203 AC: 237722 AN: 1172284 Hom.: 26494 Cov.: 24 AF XY: 0.196 AC XY: 117023 AN XY: 595890

Gnomad4 AFR exome AF: 0.197

Gnomad4 AMR exome AF: 0.255

Gnomad4 ASJ exome AF: 0.163

Gnomad4 EAS exome AF: 0.0172

Gnomad4 SAS exome AF: 0.0615

Gnomad4 FIN exome AF: 0.212

Gnomad4 NFE exome AF: 0.224

Gnomad4 OTH exome AF: 0.187

GnomAD4 genome AF: 0.186 AC: 28350 AN: 152118 Hom.: 2810 Cov.: 32 AF XY: 0.181 AC XY: 13459 AN XY: 74368

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.0530

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.168

Alfa AF: 0.199 Hom.: 579

Bravo AF: 0.190

Asia WGS AF: 0.0510 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.9
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11015624; hg19: chr10-27538569; COSMIC: COSV52632178;