Genetic Variant KRT8P2:n.241C>T (chr14-43541586-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000556193.2(KRT8P2):n.241C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000321 in 311,046 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000032 ( 0 hom. )

Consequence

KRT8P2
ENST00000556193.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.49

Variant links:

Genes affected

KRT8P2 (HGNC:20282): (keratin 8 pseudogene 2)

KRT8P2 links:

ENSG00000304974 (HGNC:):

ENSG00000304974 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRT8P2		n.43541586G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
KRT8P2	ENST00000556193.2 link	n.241C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000304974	ENST00000807481.1 link	n.401-68424C>T	intron_variant	Intron 1 of 3
ENSG00000304974	ENST00000807483.1 link	n.245+5920C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000321

AC:

AN:

311046

Hom.:

Cov.:

AF XY:

0.00000608

AC XY:

AN XY:

164602

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

8712

American (AMR)

AF:

0.00

AC:

AN:

12858

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8942

East Asian (EAS)

AF:

0.00

AC:

AN:

19766

South Asian (SAS)

AF:

0.0000316

AC:

AN:

31622

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20978

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1340

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

188958

Other (OTH)

AF:

0.00

AC:

AN:

17870

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

1503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

5.6

(source)

DANN

Benign

0.77

PhyloP100

2.5

Splicing

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

Publications

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chr14-43541586-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

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