rs1979736

Variant names:

• chr3-47190502-G-A
• rs1979736
• ENST00000429315.3:n.329+21106G>A

Variant summary

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

The ENST00000429315.3(KIF9-AS1):​n.329+21106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.958 in 152,196 control chromosomes in the GnomAD database, including 70,139 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 0.96 (70139 hom., cov: 31)
• Consequence: KIF9-AS1 ENST00000429315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 2 publications found

Genes affected

KIF9-AS1 (HGNC:26822): (KIF9 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429315.3. 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
	KIF9-AS1	NR_033373.1		n.456+21106G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF9-AS1	ENST00000429315.3	TSL:2	n.329+21106G>A		intron	N/A
	KIF9-AS1	ENST00000723160.1		n.511+21106G>A		intron	N/A
	KIF9-AS1	ENST00000723161.1		n.369+25905G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.958 AC: 145666 AN: 152078 Hom.: 70093 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.984

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.958 AC: 145771 AN: 152196 Hom.: 70139 Cov.: 31 AF XY: 0.959 AC XY: 71395 AN XY: 74446

African (AFR) AF: 0.855 AC: 35468 AN: 41490

American (AMR) AF: 0.984 AC: 15030 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3456 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5182 AN: 5182

South Asian (SAS) AF: 1.00 AC: 4822 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10612 AN: 10612

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67956 AN: 68026

Other (OTH) AF: 0.966 AC: 2043 AN: 2114

Alfa AF: 0.984 Hom.: 27429

Bravo AF: 0.952

Asia WGS AF: 0.995 AC: 3459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.42
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs1979736; hg19: chr3-47231992;