rs532701253

Variant names:

• chr11-62664891-A-G
• rs532701253
• NM_001286086.2:c.122T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-62664891-A-G
• chr11-62664891-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001286086.2(C11orf98):​c.122T>C​(p.Ile41Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000626 in 1,437,836 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000063 (0 hom.)
• Consequence: C11orf98 NM_001286086.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.76

Genes affected

C11orf98 (HGNC:51238): (chromosome 11 open reading frame 98) This gene shares three exons in common with another gene, LBH domain containing 1 (GeneID:79081), but the encoded protein uses a reading frame that is different from that of the LBH domain containing 1 gene. [provided by RefSeq, Nov 2017]

ENSG00000255432 (HGNC:):

LBHD1 (HGNC:28351): (LBH domain containing 1) This gene shares three exons in common with another gene, chromosome 11 open reading frame 98 (GeneID:102288414), but the encoded protein uses a reading frame that is different from that of the chromosome 11 open reading frame 98 gene. [provided by RefSeq, Nov 2017]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.42190337).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C11orf98	NM_001286086.2	c.122T>C	p.Ile41Thr	missense_variant	Exon 2 of 4	ENST00000524958.6	NP_001273015.1
LBHD1	NM_024099.5	c.621T>C	p.Asp207Asp	synonymous_variant	Exon 5 of 7	ENST00000354588.8	NP_077004.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C11orf98	ENST00000524958.6	c.122T>C	p.Ile41Thr	missense_variant	Exon 2 of 4	2	NM_001286086.2	ENSP00000432523.2
ENSG00000255432	ENST00000528405.1	c.122T>C	p.Ile41Thr	missense_variant	Exon 2 of 4	4		ENSP00000435188.1
LBHD1	ENST00000354588.8	c.621T>C	p.Asp207Asp	synonymous_variant	Exon 5 of 7	1	NM_024099.5	ENSP00000346600.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000626 AC: 9 AN: 1437836 Hom.: 0 Cov.: 31 AF XY: 0.00000841 AC XY: 6 AN XY: 713136

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000241

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000545

Gnomad4 OTH exome AF: 0.0000168

GnomAD4 genome Cov.: 31

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.00 AC: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Uncertain	-0.070
CADD	Benign	22
DANN	Benign	0.97
DEOGEN2	Benign	0.021	.;.;T
Eigen	Uncertain	0.20
Eigen_PC	Benign	0.20
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.74	T;T;T
M_CAP	Benign	0.025	D
MetaRNN	Benign	0.42	T;T;T
MetaSVM	Benign	-0.85	T
PROVEAN	Benign	-1.2	N;N;N
REVEL	Uncertain	0.34
Sift	Benign	0.31	T;T;T
Sift4G	Benign	0.27	T;T;T
Vest4		0.63
MVP		0.40
MPC		0.46
ClinPred		0.52	D
GERP RS		4.8
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.0
Varity_R		0.24
gMVP		0.11

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: rs532701253; hg19: chr11-62432363;