chr11-109425824-A-G

Variant names:

• chr11-109425824-A-G
• rs7116461
• NM_207645.4:c.*1597A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

LINC02715 (HGNC:54232): (long intergenic non-protein coding RNA 2715)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
C11orf87	NM_207645.4	c.*1597A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000327419.7	NP_997528.2
C11orf87	XM_011542817.3	c.*1597A>G		3_prime_UTR_variant	Exon 2 of 2		XP_011541119.1
C11orf87	XM_011542818.3	c.*1597A>G		3_prime_UTR_variant	Exon 2 of 2		XP_011541120.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C11orf87	ENST00000327419.7	c.*1597A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_207645.4	ENSP00000331581.6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.506 AC: 81 AN: 160

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.571 AC: 8 AN: 14

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.387 AC: 16033 AN: 41460

American (AMR) AF: 0.450 AC: 6869 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3468

East Asian (EAS) AF: 0.360 AC: 1848 AN: 5138

South Asian (SAS) AF: 0.292 AC: 1408 AN: 4820

European-Finnish (FIN) AF: 0.464 AC: 4893 AN: 10548

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25800 AN: 67940

Other (OTH) AF: 0.373 AC: 786 AN: 2110

Alfa AF: 0.384 Hom.: 3270

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
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7116461; hg19: chr11-109296550;