rs377479943

Variant names:

• chr2-27442591-G-A
• rs377479943
• NM_173853.4:c.41G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-27442591-G-A
• chr2-27442591-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_173853.4(KRTCAP3):​c.41G>A​(p.Gly14Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. G14V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KRTCAP3 NM_173853.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.28
• Publications: 1 publications found

Genes affected

KRTCAP3 (HGNC:28943): (keratinocyte associated protein 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173853.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRTCAP3	NM_173853.4	MANE Select	c.41G>A	p.Gly14Glu	missense	Exon 2 of 7	NP_776252.2	Q53RY4-1
	KRTCAP3	NM_001168364.2		c.41G>A	p.Gly14Glu	missense	Exon 2 of 7	NP_001161836.1	Q53RY4-1
	KRTCAP3	NM_001321325.2		c.41G>A	p.Gly14Glu	missense	Exon 2 of 7	NP_001308254.1	Q53RY4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRTCAP3	ENST00000288873.7	TSL:1 MANE Select	c.41G>A	p.Gly14Glu	missense	Exon 2 of 7	ENSP00000288873.3	Q53RY4-1
	KRTCAP3	ENST00000543753.5	TSL:5	c.41G>A	p.Gly14Glu	missense	Exon 2 of 7	ENSP00000442400.1	Q53RY4-1
	KRTCAP3	ENST00000872248.1		c.41G>A	p.Gly14Glu	missense	Exon 2 of 7	ENSP00000542307.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00 AC: 0 AN: 154628 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.62
BayesDel_addAF	Benign	-0.060	T
BayesDel_noAF	Benign	-0.32
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.011	T
Eigen	Uncertain	0.20
Eigen_PC	Benign	0.16
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Benign	0.73	T
M_CAP	Pathogenic	0.30	D
MetaRNN	Uncertain	0.72	D
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.5	L
PhyloP100		7.3
PrimateAI	Pathogenic	0.91	D
PROVEAN	Benign	-0.29	N
REVEL	Benign	0.22
Sift	Benign	0.16	T
Sift4G	Benign	0.74	T
Polyphen		1.0	D
Vest4		0.79
MutPred		0.39		Loss of MoRF binding (P = 0.0311)
MVP		0.53
MPC		0.69
ClinPred		0.95	D
GERP RS		4.1
PromoterAI		0.014	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Varity_R		0.13
gMVP		0.58
Mutation Taster		=65/35	polymorphism

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: rs377479943; hg19: chr2-27665458;