1-155171470-C-T

Variant names:

• chr1-155171470-C-T
• rs4971092
• NM_173852.4:c.223+1095G>A

Variant summary

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

The ENST00000295682.6(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 ENST00000295682.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000295682.6. 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.223+1095G>A		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.223+1095G>A		intron	N/A	ENSP00000295682.5
	ENSG00000273088	ENST00000473363.3	TSL:5	c.534+1095G>A		intron	N/A	ENSP00000477381.3
	KRTCAP2	ENST00000487350.5	TSL:1	n.565+1095G>A		intron	N/A

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

African (AFR) AF: 0.984 AC: 15540 AN: 15792

American (AMR) AF: 0.894 AC: 881 AN: 986

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 4366 AN: 5150

East Asian (EAS) AF: 0.990 AC: 3597 AN: 3634

South Asian (SAS) AF: 0.852 AC: 14032 AN: 16460

European-Finnish (FIN) AF: 0.891 AC: 246 AN: 276

Middle Eastern (MID) AF: 0.850 AC: 1378 AN: 1622

European-Non Finnish (NFE) AF: 0.879 AC: 669860 AN: 761766

Other (OTH) AF: 0.893 AC: 24379 AN: 27306

GnomAD4 genome AF: 0.908 AC: 137078 AN: 150958 Hom.: 62391 Cov.: 26 AF XY: 0.907 AC XY: 66821 AN XY: 73676

African (AFR) AF: 0.977 AC: 39899 AN: 40848

American (AMR) AF: 0.885 AC: 13409 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2906 AN: 3470

East Asian (EAS) AF: 0.988 AC: 5099 AN: 5162

South Asian (SAS) AF: 0.861 AC: 4103 AN: 4764

European-Finnish (FIN) AF: 0.899 AC: 9321 AN: 10372

Middle Eastern (MID) AF: 0.873 AC: 255 AN: 292

European-Non Finnish (NFE) AF: 0.875 AC: 59433 AN: 67892

Other (OTH) AF: 0.883 AC: 1850 AN: 2096

Alfa AF: 0.879 Hom.: 64179

Bravo AF: 0.910

Asia WGS AF: 0.926 AC: 3219 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.0
DANN	Benign	0.79
PhyloP100		0.10
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: rs4971092; hg19: chr1-155143946;