14-43541586-G-T

Variant names:

• chr14-43541586-G-T
• rs8005625
• ENST00000556193.2:n.241C>A

Variant summary

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

The ENST00000556193.2(KRT8P2):​n.241C>A 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 0.144 in 462,638 control chromosomes in the GnomAD database, including 5,155 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 0.14 (1501 hom., cov: 32)
  • Exomes 𝑓: 0.15 (3654 hom.)
• Consequence: KRT8P2 ENST00000556193.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49
• Publications: 4 publications found

Genes affected

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

ENSG00000304974 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556193.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRT8P2	ENST00000556193.2	TSL:6	n.241C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000304974	ENST00000807481.1		n.401-68424C>A		intron	N/A
	ENSG00000304974	ENST00000807483.1		n.245+5920C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20736 AN: 152056 Hom.: 1500 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.127

GnomAD4 exome AF: 0.148 AC: 45846 AN: 310464 Hom.: 3654 Cov.: 3 AF XY: 0.147 AC XY: 24233 AN XY: 164308

African (AFR) AF: 0.109 AC: 950 AN: 8704

American (AMR) AF: 0.0738 AC: 948 AN: 12842

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 993 AN: 8936

East Asian (EAS) AF: 0.120 AC: 2365 AN: 19728

South Asian (SAS) AF: 0.147 AC: 4623 AN: 31554

European-Finnish (FIN) AF: 0.156 AC: 3265 AN: 20938

Middle Eastern (MID) AF: 0.132 AC: 176 AN: 1336

European-Non Finnish (NFE) AF: 0.159 AC: 29944 AN: 188594

Other (OTH) AF: 0.145 AC: 2582 AN: 17832

GnomAD4 genome AF: 0.136 AC: 20745 AN: 152174 Hom.: 1501 Cov.: 32 AF XY: 0.134 AC XY: 9973 AN XY: 74398

African (AFR) AF: 0.109 AC: 4520 AN: 41540

American (AMR) AF: 0.0932 AC: 1425 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3470

East Asian (EAS) AF: 0.148 AC: 764 AN: 5164

South Asian (SAS) AF: 0.153 AC: 737 AN: 4826

European-Finnish (FIN) AF: 0.149 AC: 1583 AN: 10594

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10978 AN: 67978

Other (OTH) AF: 0.125 AC: 263 AN: 2110

Alfa AF: 0.138 Hom.: 1503

Bravo AF: 0.129

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs8005625; hg19: chr14-44010789;