1-216246662-G-T

Variant names:

• chr1-216246662-G-T
• rs397518006
• NM_206933.4:c.2732C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1 PM2 BP4_Moderate BP6_Moderate

The NM_206933.4(USH2A):​c.2732C>A​(p.Thr911Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T911T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: USH2A NM_206933.4 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.41

Genes affected

USH2A (HGNC:12601): (usherin) This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM1: In a domain Laminin EGF-like 8 (size 50) in uniprot entity USH2A_HUMAN there are 13 pathogenic changes around while only 4 benign (76%) in NM_206933.4
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2163639).
• BP6: Variant 1-216246662-G-T is Benign according to our data. Variant chr1-216246662-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 48490.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-216246662-G-T is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USH2A	NM_206933.4	c.2732C>A	p.Thr911Asn	missense_variant	Exon 13 of 72	ENST00000307340.8	NP_996816.3
USH2A	NM_007123.6	c.2732C>A	p.Thr911Asn	missense_variant	Exon 13 of 21		NP_009054.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USH2A	ENST00000307340.8	c.2732C>A	p.Thr911Asn	missense_variant	Exon 13 of 72	1	NM_206933.4	ENSP00000305941.3
USH2A	ENST00000366942.3	c.2732C>A	p.Thr911Asn	missense_variant	Exon 13 of 21	1		ENSP00000355909.3
USH2A	ENST00000674083.1	c.2732C>A	p.Thr911Asn	missense_variant	Exon 13 of 73			ENSP00000501296.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 14, 2011

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Thr911Asn in exon 13 of USH2A: This variant has been reported in 1 individual wi th retinitis pigmentosa (Seyedahmadi 2004, McGee 2010). However, this variant is not expected to have clinical significance because the Thr911 residue is not we ll conserved, even in mammals, and the Thr911Asn variant was identified in an in dividual who has an alternate etiology for Usher syndrome. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	14
DANN	Uncertain	0.98
DEOGEN2	Benign	0.078	T;.
Eigen	Benign	-0.15
Eigen_PC	Benign	-0.13
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.55	T;T
M_CAP	Benign	0.022	T
MetaRNN	Benign	0.22	T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	1.2	L;L
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-1.7	N;N
REVEL	Benign	0.19
Sift	Benign	0.066	T;T
Sift4G	Uncertain	0.028	D;T
Polyphen		0.97	D;P
Vest4		0.22
MutPred		0.43		Gain of disorder (P = 0.1288);Gain of disorder (P = 0.1288);
MVP		0.93
MPC		0.036
ClinPred		0.54	D
GERP RS		3.1
Varity_R		0.10
gMVP		0.31

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: rs397518006; hg19: chr1-216420004; COSMIC: COSV56358921;