11-27484130-C-T

Variant names:

• chr11-27484130-C-T
• rs10835187

Variant summary

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

The variant allele was found at a frequency of 0.478 in 507,172 control chromosomes in the GnomAD database, including 62,978 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 0.42 (15783 hom., cov: 32)
  • Exomes 𝑓: 0.50 (47195 hom.)
• Consequence: RPL37AP7 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 37 publications found

Genes affected

RPL37AP7 (HGNC:35888):

LGR4-AS1 (HGNC:40629): (LGR4 antisense RNA 1)

ENSG00000242527 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL37AP7		n.27484130C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LGR4-AS1	ENST00000715842.1	n.431+10934C>T		intron_variant	Intron 3 of 3
ENSG00000242527	ENST00000496450.1	n.*2C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63448 AN: 151876 Hom.: 15781 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.504 AC: 178916 AN: 355178 Hom.: 47195 Cov.: 0 AF XY: 0.512 AC XY: 103203 AN XY: 201470

African (AFR) AF: 0.142 AC: 1452 AN: 10258

American (AMR) AF: 0.282 AC: 8925 AN: 31648

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 6284 AN: 11386

East Asian (EAS) AF: 0.444 AC: 6330 AN: 14272

South Asian (SAS) AF: 0.507 AC: 31701 AN: 62512

European-Finnish (FIN) AF: 0.542 AC: 12732 AN: 23498

Middle Eastern (MID) AF: 0.543 AC: 680 AN: 1252

European-Non Finnish (NFE) AF: 0.557 AC: 102386 AN: 183798

Other (OTH) AF: 0.509 AC: 8426 AN: 16554

GnomAD4 genome AF: 0.417 AC: 63439 AN: 151994 Hom.: 15783 Cov.: 32 AF XY: 0.419 AC XY: 31126 AN XY: 74274

African (AFR) AF: 0.147 AC: 6085 AN: 41490

American (AMR) AF: 0.347 AC: 5298 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1911 AN: 3468

East Asian (EAS) AF: 0.458 AC: 2343 AN: 5120

South Asian (SAS) AF: 0.495 AC: 2382 AN: 4814

European-Finnish (FIN) AF: 0.564 AC: 5954 AN: 10556

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37876 AN: 67962

Other (OTH) AF: 0.438 AC: 926 AN: 2114

Alfa AF: 0.473 Hom.: 15587

Bravo AF: 0.385

Asia WGS AF: 0.461 AC: 1603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.021
DANN	Benign	0.79
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10835187; hg19: chr11-27505677; COSMIC: COSV72467455;