1-155171470-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

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]

ACMG classification

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/exons	MANE	UniProt
KRTCAP2	NM_173852.4	c.223+1095G>A		intron_variant		ENST00000295682.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRTCAP2	ENST00000295682.6	c.223+1095G>A		intron_variant		1	NM_173852.4	P1

Frequencies

GnomAD3 genomes AF: 0.908 AC: 136970 AN: 150840 Hom.: 62340 Cov.: 26

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.: 33 AF XY: 0.880 AC XY: 338570 AN XY: 384698

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.: 26 AF XY: 0.907 AC XY: 66821 AN XY: 73676

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

Other links and lift over

dbSNP: rs4971092; hg19: chr1-155143946;