rs1316185449

Variant names:

• chr1-151518590-C-A
• NM_020770.3:c.71C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-151518590-C-A
• chr1-151518590-C-T

Variant summary

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

The NM_020770.3(CGN):​c.71C>A​(p.Thr24Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,868 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. T24A) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: CGN NM_020770.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.80

Genes affected

CGN (HGNC:17429): (cingulin) Enables cadherin binding activity. Predicted to act upstream of or within bicellular tight junction assembly; epithelial cell morphogenesis; and microtubule cytoskeleton organization. Located in bicellular tight junction and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=0.2169402).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CGN	NM_020770.3	c.71C>A	p.Thr24Lys	missense_variant	Exon 2 of 21	ENST00000271636.12	NP_065821.1
CGN	XM_005245365.6	c.71C>A	p.Thr24Lys	missense_variant	Exon 2 of 21		XP_005245422.1
CGN	XR_921902.3	n.214C>A		non_coding_transcript_exon_variant	Exon 2 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CGN	ENST00000271636.12	c.71C>A	p.Thr24Lys	missense_variant	Exon 2 of 21	1	NM_020770.3	ENSP00000271636.7
CGN	ENST00000502442.1	c.71C>A	p.Thr24Lys	missense_variant	Exon 2 of 2	1		ENSP00000422299.1
CGN	ENST00000505188.5	c.71C>A	p.Thr24Lys	missense_variant	Exon 2 of 2	1		ENSP00000425532.1
CGN	ENST00000427934.2	c.71C>A	p.Thr24Lys	missense_variant	Exon 3 of 3	5		ENSP00000410836.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461868 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727236

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: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.042	T
BayesDel_noAF	Benign	-0.18
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.015	.;.;T;.
Eigen	Benign	0.032
Eigen_PC	Benign	0.18
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Benign	0.74	.;T;T;.
M_CAP	Benign	0.015	T
MetaRNN	Benign	0.22	T;T;T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Uncertain	0.72	T
PROVEAN	Benign	-0.84	N;N;N;N
REVEL	Benign	0.12
Sift	Benign	0.095	T;T;T;T
Sift4G	Uncertain	0.032	D;D;D;T
Vest4		0.40
MVP		0.41
MPC		0.51
ClinPred		0.91	D
GERP RS		5.0
gMVP		0.13

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr1-151491066;