rs61388742

Variant names:

• chr8-1817259-T-C
• rs61388742
• ENST00000635855.1:n.544-26094T>C

Variant summary

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

The ENST00000635855.1(KBTBD11-OT1):​n.544-26094T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 516,166 control chromosomes in the GnomAD database, including 2,251 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 0.094 (689 hom., cov: 33)
  • Exomes 𝑓: 0.081 (1562 hom.)
• Consequence: KBTBD11-OT1 ENST00000635855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 13 publications found

Genes affected

KBTBD11-OT1 (HGNC:):

MIR596 (HGNC:32852): (microRNA 596) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635855.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR596	NR_030326.1		n.29T>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KBTBD11-OT1	ENST00000635855.1	TSL:5	n.544-26094T>C		intron	N/A	ENSP00000489726.1
	MIR596	ENST00000385091.1	TSL:6	n.29T>C		non_coding_transcript_exon	Exon 1 of 1
	KBTBD11-OT1	ENST00000635773.1	TSL:5	n.496-40701T>C		intron	N/A	ENSP00000490620.1

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14367 AN: 152144 Hom.: 689 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.102

GnomAD2 exomes AF: 0.0813 AC: 19664 AN: 242000 AF XY: 0.0794

Gnomad AFR exome AF: 0.104

Gnomad AMR exome AF: 0.0539

Gnomad ASJ exome AF: 0.0969

Gnomad EAS exome AF: 0.000170

Gnomad FIN exome AF: 0.106

Gnomad NFE exome AF: 0.109

Gnomad OTH exome AF: 0.0967

GnomAD4 exome AF: 0.0811 AC: 29522 AN: 363904 Hom.: 1562 Cov.: 0 AF XY: 0.0761 AC XY: 15654 AN XY: 205804

African (AFR) AF: 0.0953 AC: 963 AN: 10110

American (AMR) AF: 0.0544 AC: 1897 AN: 34856

Ashkenazi Jewish (ASJ) AF: 0.0966 AC: 1111 AN: 11504

East Asian (EAS) AF: 0.00 AC: 0 AN: 12140

South Asian (SAS) AF: 0.0153 AC: 992 AN: 64800

European-Finnish (FIN) AF: 0.106 AC: 3404 AN: 32088

Middle Eastern (MID) AF: 0.111 AC: 312 AN: 2800

European-Non Finnish (NFE) AF: 0.108 AC: 19415 AN: 179760

Other (OTH) AF: 0.0901 AC: 1428 AN: 15846

GnomAD4 genome AF: 0.0944 AC: 14368 AN: 152262 Hom.: 689 Cov.: 33 AF XY: 0.0932 AC XY: 6941 AN XY: 74462

African (AFR) AF: 0.101 AC: 4179 AN: 41542

American (AMR) AF: 0.0781 AC: 1195 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0133 AC: 64 AN: 4828

European-Finnish (FIN) AF: 0.119 AC: 1263 AN: 10612

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7092 AN: 68014

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.0976 Hom.: 454

Bravo AF: 0.0929

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.24
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs61388742; hg19: chr8-1765425;