NM_173852.4:c.224-550A>T

Variant names:

• chr1-155170407-T-A
• rs4971088
• NM_173852.4:c.224-550A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173852.4(KRTCAP2):​c.224-550A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 150,220 control chromosomes in the GnomAD database, including 24,112 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 0.56 (24097 hom., cov: 28)
  • Exomes 𝑓: 0.43 (15 hom.)
• Consequence: KRTCAP2 NM_173852.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.906
• Publications: 17 publications found

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]

ENSG00000273088 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173852.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRTCAP2	NM_173852.4	MANE Select	c.224-550A>T		intron	N/A	NP_776251.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRTCAP2	ENST00000295682.6	TSL:1 MANE Select	c.224-550A>T		intron	N/A	ENSP00000295682.5
	ENSG00000273088	ENST00000473363.3	TSL:5	c.535-550A>T		intron	N/A	ENSP00000477381.3
	KRTCAP2	ENST00000487350.5	TSL:1	n.566-550A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 83820 AN: 149994 Hom.: 24052 Cov.: 28

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.531

GnomAD4 exome AF: 0.426 AC: 52 AN: 122 Hom.: 15 Cov.: 0 AF XY: 0.443 AC XY: 31 AN XY: 70

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 5 AN: 10

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.833 AC: 5 AN: 6

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.360 AC: 36 AN: 100

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.559 AC: 83911 AN: 150098 Hom.: 24097 Cov.: 28 AF XY: 0.560 AC XY: 40953 AN XY: 73070

African (AFR) AF: 0.673 AC: 27462 AN: 40812

American (AMR) AF: 0.600 AC: 9023 AN: 15032

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1413 AN: 3456

East Asian (EAS) AF: 0.803 AC: 4099 AN: 5104

South Asian (SAS) AF: 0.532 AC: 2536 AN: 4766

European-Finnish (FIN) AF: 0.526 AC: 5239 AN: 9954

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32453 AN: 67686

Other (OTH) AF: 0.529 AC: 1109 AN: 2096

Alfa AF: 0.355 Hom.: 920

Bravo AF: 0.574

Asia WGS AF: 0.677 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.34
PhyloP100		-0.91
Mutation Taster		=100/0	polymorphism (auto)

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: rs4971088; hg19: chr1-155142883;