rs1809667

Variant names:

• chr11-1598629-C-A
• rs1809667
• ENST00000424148.1:n.1710C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000424148.1(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 ENST00000424148.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424148.1. 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
	KRTAP5-AS1	NR_021489.2		n.1710C>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRTAP5-AS1	ENST00000424148.1	TSL:2	n.1710C>A		non_coding_transcript_exon	Exon 2 of 2
	KRTAP5-AS1	ENST00000792906.1		n.214-13736C>A		intron	N/A

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

African (AFR) AF: 0.248 AC: 1706 AN: 6882

American (AMR) AF: 0.116 AC: 1038 AN: 8954

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 1292 AN: 6340

East Asian (EAS) AF: 0.105 AC: 1292 AN: 12304

South Asian (SAS) AF: 0.167 AC: 4329 AN: 25918

European-Finnish (FIN) AF: 0.108 AC: 1218 AN: 11306

Middle Eastern (MID) AF: 0.211 AC: 191 AN: 904

European-Non Finnish (NFE) AF: 0.140 AC: 17878 AN: 127698

Other (OTH) AF: 0.153 AC: 1829 AN: 11934

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

African (AFR) AF: 0.259 AC: 10738 AN: 41514

American (AMR) AF: 0.143 AC: 2189 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3468

East Asian (EAS) AF: 0.117 AC: 604 AN: 5176

South Asian (SAS) AF: 0.154 AC: 740 AN: 4816

European-Finnish (FIN) AF: 0.106 AC: 1127 AN: 10594

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10091 AN: 67990

Other (OTH) AF: 0.167 AC: 353 AN: 2114

Alfa AF: 0.151 Hom.: 3802

Bravo AF: 0.183

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.45
DANN	Benign	0.79
PhyloP100		-2.1
PromoterAI		0.00010	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1809667;

hg19: chr11-1619859;