rs936268580

Variant names:

• chr8-94642005-C-A
• NM_017697.4:c.182C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-94642005-C-A
• chr8-94642005-C-G
• chr8-94642005-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_017697.4(ESRP1):​c.182C>A​(p.Thr61Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,624 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T61M) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: ESRP1 NM_017697.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.63

Genes affected

ESRP1 (HGNC:25966): (epithelial splicing regulatory protein 1) ESPR1 is an epithelial cell-type-specific splicing regulator (Warzecha et al., 2009 [PubMed 19285943]).[supplied by OMIM, Aug 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.24026415).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ESRP1	NM_017697.4	c.182C>A	p.Thr61Lys	missense_variant	Exon 2 of 16	ENST00000433389.8	NP_060167.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ESRP1	ENST00000433389.8	c.182C>A	p.Thr61Lys	missense_variant	Exon 2 of 16	1	NM_017697.4	ENSP00000405738.2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461624 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 727098

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Benign	-0.093	T
BayesDel_noAF	Benign	-0.37
CADD	Uncertain	26
DANN	Uncertain	0.98
DEOGEN2	Benign	0.067	.;T;T;.;.;.
Eigen	Benign	-0.43
Eigen_PC	Benign	-0.23
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Uncertain	0.97	D;.;D;D;D;D
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.24	T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.0	L;L;L;L;L;.
PrimateAI	Uncertain	0.75	T
PROVEAN	Benign	-1.4	N;N;.;N;.;N
REVEL	Benign	0.19
Sift	Benign	0.25	T;T;.;T;.;T
Sift4G	Benign	0.31	T;T;.;T;.;T
Polyphen		0.0020, 0.014	.;B;B;B;B;.
Vest4		0.45
MutPred		0.48		Gain of ubiquitination at T61 (P = 0.0117);Gain of ubiquitination at T61 (P = 0.0117);Gain of ubiquitination at T61 (P = 0.0117);Gain of ubiquitination at T61 (P = 0.0117);Gain of ubiquitination at T61 (P = 0.0117);Gain of ubiquitination at T61 (P = 0.0117);
MVP		0.36
MPC		0.74
ClinPred		0.80	D
GERP RS		4.1
Varity_R		0.27
gMVP		0.75

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-95654233;