2-27444317-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001168364.2(KRTCAP3):c.*5+256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 684,038 control chromosomes in the GnomAD database, including 1,897 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.089 (897 hom., cov: 32)
  • Exomes 𝑓: 0.053 (1000 hom.)
• Consequence: KRTCAP3 NM_001168364.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.27

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

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-27444317-G-A is Benign according to our data. Variant chr2-27444317-G-A is described in ClinVar as [Benign]. Clinvar id is 1235989.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRTCAP3	NM_001168364.2	c.*5+256G>A		intron_variant
KRTCAP3	NM_173853.4			downstream_gene_variant		ENST00000288873.7
KRTCAP3	NM_001321325.2			downstream_gene_variant
KRTCAP3	XM_047443704.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRTCAP3	ENST00000288873.7			downstream_gene_variant		1	NM_173853.4	P1

Frequencies

GnomAD3 genomes AF: 0.0888 AC: 13480 AN: 151804 Hom.: 890 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0295

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0554

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0542

Gnomad OTH AF: 0.0852

GnomAD4 exome AF: 0.0534 AC: 28439 AN: 532116 Hom.: 1000 Cov.: 7 AF XY: 0.0536 AC XY: 15071 AN XY: 281026

Gnomad4 AFR exome AF: 0.192

Gnomad4 AMR exome AF: 0.0418

Gnomad4 ASJ exome AF: 0.0295

Gnomad4 EAS exome AF: 0.000220

Gnomad4 SAS exome AF: 0.0613

Gnomad4 FIN exome AF: 0.0383

Gnomad4 NFE exome AF: 0.0544

Gnomad4 OTH exome AF: 0.0622

GnomAD4 genome AF: 0.0889 AC: 13511 AN: 151922 Hom.: 897 Cov.: 32 AF XY: 0.0850 AC XY: 6313 AN XY: 74246

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0295

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0561

Gnomad4 FIN AF: 0.0385

Gnomad4 NFE AF: 0.0542

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0741 Hom.: 96

Bravo AF: 0.0962

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 16, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	17
Dann	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.48		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.48		Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs62131871; hg19: chr2-27667184;