10-27250013-T-C

Variant names:

• chr10-27250013-T-C
• rs590142
• ENST00000284414.4:n.550A>G

Variant summary

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

The ENST00000284414.4(ENSG00000293149):​n.550A>G 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 0.2 in 1,257,530 control chromosomes in the GnomAD database, including 31,731 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 0.21 (3993 hom., cov: 31)
  • Exomes 𝑓: 0.20 (27738 hom.)
• Consequence: ENSG00000293149 ENST00000284414.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 7 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC37A6P	NR_003525.2	n.2294A>G		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.550A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
LRRC37A6P	ENST00000448648.2	n.1781A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000262412	ENST00000574842.2	n.298-45T>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32177 AN: 151834 Hom.: 3980 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.236

GnomAD2 exomes AF: 0.258 AC: 64540 AN: 250212 AF XY: 0.266

Gnomad AFR exome AF: 0.102

Gnomad AMR exome AF: 0.214

Gnomad ASJ exome AF: 0.238

Gnomad EAS exome AF: 0.467

Gnomad FIN exome AF: 0.237

Gnomad NFE exome AF: 0.232

Gnomad OTH exome AF: 0.250

GnomAD4 exome AF: 0.199 AC: 219872 AN: 1105578 Hom.: 27738 Cov.: 19 AF XY: 0.209 AC XY: 117939 AN XY: 564834

African (AFR) AF: 0.0840 AC: 2339 AN: 27856

American (AMR) AF: 0.214 AC: 9409 AN: 43986

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 5351 AN: 23770

East Asian (EAS) AF: 0.494 AC: 18426 AN: 37288

South Asian (SAS) AF: 0.359 AC: 27854 AN: 77630

European-Finnish (FIN) AF: 0.230 AC: 12065 AN: 52356

Middle Eastern (MID) AF: 0.244 AC: 1222 AN: 5000

European-Non Finnish (NFE) AF: 0.168 AC: 133034 AN: 789696

Other (OTH) AF: 0.212 AC: 10172 AN: 47996

GnomAD4 genome AF: 0.212 AC: 32202 AN: 151952 Hom.: 3993 Cov.: 31 AF XY: 0.218 AC XY: 16173 AN XY: 74258

African (AFR) AF: 0.101 AC: 4194 AN: 41438

American (AMR) AF: 0.247 AC: 3767 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3472

East Asian (EAS) AF: 0.472 AC: 2421 AN: 5126

South Asian (SAS) AF: 0.399 AC: 1921 AN: 4818

European-Finnish (FIN) AF: 0.243 AC: 2564 AN: 10552

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15711 AN: 67958

Other (OTH) AF: 0.244 AC: 515 AN: 2110

Alfa AF: 0.149 Hom.: 774

Bravo AF: 0.204

Asia WGS AF: 0.432 AC: 1500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs590142; hg19: chr10-27538942; COSMIC: COSV52632069;