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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715842.1. You can select a different transcript below to see updated ACMG assignments.

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
	LGR4-AS1	ENST00000715842.1		n.431+10934C>T		intron	N/A
	ENSG00000242527	ENST00000496450.1	TSL:6	n.*2C>T		downstream_gene	N/A

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 v4.9

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;