rs7116461

Positions:

• chr11-109425824-A-G

Variant summary

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

The NM_207645.4(C11orf87):​c.*1597A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,142 control chromosomes in the GnomAD database, including 11,629 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 0.39 (11606 hom., cov: 32)
  • Exomes 𝑓: 0.51 (23 hom.)
• Consequence: C11orf87 NM_207645.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

Genes affected

C11orf87 (HGNC:33788): (chromosome 11 open reading frame 87) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C11orf87	NM_207645.4	c.*1597A>G		3_prime_UTR_variant	2/2	ENST00000327419.7	NP_997528.2
C11orf87	XM_011542817.3	c.*1597A>G		3_prime_UTR_variant	2/2		XP_011541119.1
C11orf87	XM_011542818.3	c.*1597A>G		3_prime_UTR_variant	2/2		XP_011541120.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C11orf87	ENST00000327419.7	c.*1597A>G		3_prime_UTR_variant	2/2	1	NM_207645.4	ENSP00000331581	P1
	ENST00000532992.5	n.428-60756T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000532929.1	n.253-9653T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59285 AN: 151846 Hom.: 11577 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.375

GnomAD4 exome AF: 0.511 AC: 90 AN: 176 Hom.: 23 Cov.: 0 AF XY: 0.561 AC XY: 46 AN XY: 82

Gnomad4 FIN exome AF: 0.506

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.391 AC: 59354 AN: 151966 Hom.: 11606 Cov.: 32 AF XY: 0.394 AC XY: 29251 AN XY: 74260

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.373

Alfa AF: 0.389 Hom.: 1753

Bravo AF: 0.397

Asia WGS AF: 0.285 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	14
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7116461; hg19: chr11-109296550;