rs11015624

Variant names:

• chr10-27249640-G-A
• rs11015624
• ENST00000284414.4:n.923C>T

Variant summary

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

The ENST00000284414.4(ENSG00000293149):​n.923C>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: ENSG00000293149 ENST00000284414.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 4 publications found

Genes affected

ENSG00000293149 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LRRC37A6P	NR_003525.2	n.2667C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293149	ENST00000284414.4	n.923C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LRRC37A6P	ENST00000448648.2	n.2154C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000262412	ENST00000574842.2	n.298-418G>A		intron_variant	Intron 1 of 1	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

GnomAD2 exomes AF: 0.177 AC: 44476 AN: 250942 AF XY: 0.169

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 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

African (AFR) AF: 0.197 AC: 5451 AN: 27666

American (AMR) AF: 0.255 AC: 11258 AN: 44104

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 3962 AN: 24292

East Asian (EAS) AF: 0.0172 AC: 654 AN: 38088

South Asian (SAS) AF: 0.0615 AC: 4907 AN: 79726

European-Finnish (FIN) AF: 0.212 AC: 11121 AN: 52546

Middle Eastern (MID) AF: 0.102 AC: 369 AN: 3628

European-Non Finnish (NFE) AF: 0.224 AC: 190629 AN: 852034

Other (OTH) AF: 0.187 AC: 9371 AN: 50200

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

African (AFR) AF: 0.186 AC: 7715 AN: 41478

American (AMR) AF: 0.206 AC: 3149 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3466

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5174

South Asian (SAS) AF: 0.0530 AC: 256 AN: 4826

European-Finnish (FIN) AF: 0.195 AC: 2058 AN: 10574

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14024 AN: 67998

Other (OTH) AF: 0.168 AC: 354 AN: 2108

Alfa AF: 0.200 Hom.: 603

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

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