rs10768666

Variant names:

• chr11-1611181-A-G
• rs10768666
• ENST00000792906.1:n.214-1184A>G

Variant summary

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

The ENST00000792906.1(KRTAP5-AS1):​n.214-1184A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 151,792 control chromosomes in the GnomAD database, including 680 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 0.089 (680 hom., cov: 31)
• Consequence: KRTAP5-AS1 ENST00000792906.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRTAP5-AS1	ENST00000792906.1	n.214-1184A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0893 AC: 13549 AN: 151674 Hom.: 681 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0705

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0776

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0894 AC: 13569 AN: 151792 Hom.: 680 Cov.: 31 AF XY: 0.0880 AC XY: 6525 AN XY: 74186

African (AFR) AF: 0.110 AC: 4541 AN: 41362

American (AMR) AF: 0.0707 AC: 1073 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3468

East Asian (EAS) AF: 0.126 AC: 650 AN: 5172

South Asian (SAS) AF: 0.0858 AC: 411 AN: 4792

European-Finnish (FIN) AF: 0.0614 AC: 647 AN: 10542

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

European-Non Finnish (NFE) AF: 0.0831 AC: 5646 AN: 67966

Other (OTH) AF: 0.0768 AC: 162 AN: 2110

Alfa AF: 0.0857 Hom.: 82

Bravo AF: 0.0910

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.22
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs10768666; hg19: chr11-1632411;