chr8-1972295-G-A

Variant names:

• chr8-1972295-G-A
• rs4242546
• ENST00000517676.3:n.979C>T

Variant summary

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

The ENST00000517676.3(KBTBD11-AS1):​n.979C>T 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 0.769 in 152,120 control chromosomes in the GnomAD database, including 45,137 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 0.77 (45137 hom., cov: 32)
• Consequence: KBTBD11-AS1 ENST00000517676.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 7 publications found

Genes affected

KBTBD11-AS1 (HGNC:55530): (KBTBD11 antisense RNA 1)

KBTBD11-OT1 (HGNC:49147): (KBTBD11 overlapping transcript 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KBTBD11-AS1	NR_136274.1	n.507C>T		non_coding_transcript_exon_variant	Exon 4 of 4
KBTBD11-AS1	NR_136275.1	n.385C>T		non_coding_transcript_exon_variant	Exon 3 of 3
KBTBD11-OT1	NR_126346.1	n.235+258G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KBTBD11-AS1	ENST00000517676.3	n.979C>T		non_coding_transcript_exon_variant	Exon 3 of 3	5
KBTBD11-AS1	ENST00000650317.3	n.670C>T		non_coding_transcript_exon_variant	Exon 5 of 5
KBTBD11-AS1	ENST00000662506.1	n.650C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116966 AN: 152002 Hom.: 45111 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.708

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.769 AC: 117038 AN: 152120 Hom.: 45137 Cov.: 32 AF XY: 0.773 AC XY: 57482 AN XY: 74378

African (AFR) AF: 0.767 AC: 31829 AN: 41484

American (AMR) AF: 0.778 AC: 11892 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2736 AN: 3472

East Asian (EAS) AF: 0.808 AC: 4180 AN: 5172

South Asian (SAS) AF: 0.784 AC: 3777 AN: 4820

European-Finnish (FIN) AF: 0.797 AC: 8424 AN: 10572

Middle Eastern (MID) AF: 0.707 AC: 205 AN: 290

European-Non Finnish (NFE) AF: 0.760 AC: 51658 AN: 67992

Other (OTH) AF: 0.750 AC: 1586 AN: 2114

Alfa AF: 0.760 Hom.: 120780

Bravo AF: 0.768

Asia WGS AF: 0.817 AC: 2841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs4242546; hg19: chr8-1920461;