Genetic Variant KRTCAP2:c.223+1095G>A (chr1-155171470-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173852.4(KRTCAP2):c.223+1095G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 983,950 control chromosomes in the GnomAD database, including 386,197 homozygotes. 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: 𝑓 0.91 ( 62391 hom., cov: 26)

Exomes 𝑓: 0.88 ( 323806 hom. )

Consequence

KRTCAP2
NM_173852.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.104

Variant links:

Genes affected

KRTCAP2 (HGNC:28942): (keratinocyte associated protein 2) Enables enzyme activator activity. Involved in protein N-linked glycosylation via arginine. Is active in oligosaccharyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]

KRTCAP2 links:

ENSG00000273088 (HGNC:):

ENSG00000273088 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRTCAP2	NM_173852.4 link	c.223+1095G>A		intron_variant	Intron 3 of 4	ENST00000295682.6	NP_776251.2	Q8N6L1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRTCAP2	ENST00000295682.6 link	c.223+1095G>A		intron_variant	Intron 3 of 4	1	NM_173852.4	ENSP00000295682.5		Q8N6L1-1
ENSG00000273088	ENST00000473363.3 link	c.534+1095G>A		intron_variant	Intron 3 of 4	5		ENSP00000477381.3		V9GZ38

Frequencies

GnomAD3 genomes

AF:

0.908

AC:

136970

AN:

150840

Hom.:

62340

Cov.:

show subpopulations

Gnomad AFR

AF:

0.977

Gnomad AMI

AF:

0.886

Gnomad AMR

AF:

0.885

Gnomad ASJ

AF:

0.837

Gnomad EAS

AF:

0.988

Gnomad SAS

AF:

0.863

Gnomad FIN

AF:

0.899

Gnomad MID

AF:

0.877

Gnomad NFE

AF:

0.875

Gnomad OTH

AF:

0.884

GnomAD4 exome

AF:

0.881

AC:

734279

AN:

832992

Hom.:

323806

Cov.:

AF XY:

0.880

AC XY:

338570

AN XY:

384698

show subpopulations

Gnomad4 AFR exome

AF:

0.984

Gnomad4 AMR exome

AF:

0.894

Gnomad4 ASJ exome

AF:

0.848

Gnomad4 EAS exome

AF:

0.990

Gnomad4 SAS exome

AF:

0.852

Gnomad4 FIN exome

AF:

0.891

Gnomad4 NFE exome

AF:

0.879

Gnomad4 OTH exome

AF:

0.893

GnomAD4 genome

AF:

0.908

AC:

137078

AN:

150958

Hom.:

62391

Cov.:

AF XY:

0.907

AC XY:

66821

AN XY:

73676

show subpopulations

Gnomad4 AFR

AF:

0.977

Gnomad4 AMR

AF:

0.885

Gnomad4 ASJ

AF:

0.837

Gnomad4 EAS

AF:

0.988

Gnomad4 SAS

AF:

0.861

Gnomad4 FIN

AF:

0.899

Gnomad4 NFE

AF:

0.875

Gnomad4 OTH

AF:

0.883

Alfa

AF:

0.875

Hom.:

48332

Bravo

AF:

0.910

Asia WGS

AF:

0.926

AC:

3219

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

7.0

DANN

Benign

0.79

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over