rs1809667

Positions:

• chr11-1598629-C-A
• chr11-1598629-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_021489.2(KRTAP5-AS1):​n.1710C>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 0.158 in 364,414 control chromosomes in the GnomAD database, including 5,152 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 0.18 (2624 hom., cov: 31)
  • Exomes 𝑓: 0.14 (2528 hom.)
• Consequence: KRTAP5-AS1 NR_021489.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

Genes affected

KRTAP5-AS1 (HGNC:27877): (KRTAP5-1/KRTAP5-2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRTAP5-AS1	NR_021489.2	n.1710C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRTAP5-AS1	ENST00000424148.1	n.1710C>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26915 AN: 152056 Hom.: 2619 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.167

GnomAD4 exome AF: 0.145 AC: 30773 AN: 212240 Hom.: 2528 Cov.: 0 AF XY: 0.147 AC XY: 16408 AN XY: 111272

Gnomad4 AFR exome AF: 0.248

Gnomad4 AMR exome AF: 0.116

Gnomad4 ASJ exome AF: 0.204

Gnomad4 EAS exome AF: 0.105

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.108

Gnomad4 NFE exome AF: 0.140

Gnomad4 OTH exome AF: 0.153

GnomAD4 genome AF: 0.177 AC: 26959 AN: 152174 Hom.: 2624 Cov.: 31 AF XY: 0.173 AC XY: 12861 AN XY: 74398

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.167

Alfa AF: 0.147 Hom.: 2651

Bravo AF: 0.183

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.45
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1809667; hg19: chr11-1619859;