chr9-112606778-G-A

Variant names:

• chr9-112606778-G-A
• rs2676628
• NM_133465.4:c.1171+31527G>A

Variant summary

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

The NM_133465.4(KIAA1958):​c.1171+31527G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,154 control chromosomes in the GnomAD database, including 55,481 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 0.85 (55481 hom., cov: 31)
• Consequence: KIAA1958 NM_133465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 2 publications found

Genes affected

KIAA1958 (HGNC:23427): (KIAA1958)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_133465.4. 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
	KIAA1958	NM_133465.4	MANE Select	c.1171+31527G>A		intron	N/A	NP_597722.1
	KIAA1958	NM_001287036.2		c.1172-11093G>A		intron	N/A	NP_001273965.1
	KIAA1958	NM_001287038.2		c.1171+31527G>A		intron	N/A	NP_001273967.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1958	ENST00000337530.11	TSL:1 MANE Select	c.1171+31527G>A		intron	N/A	ENSP00000336940.6
	KIAA1958	ENST00000536272.5	TSL:1	c.1172-11093G>A		intron	N/A	ENSP00000440504.1
	KIAA1958	ENST00000374244.3	TSL:5	c.1172-11093G>A		intron	N/A	ENSP00000363362.3

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129555 AN: 152036 Hom.: 55428 Cov.: 31

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.852 AC: 129665 AN: 152154 Hom.: 55481 Cov.: 31 AF XY: 0.849 AC XY: 63145 AN XY: 74382

African (AFR) AF: 0.898 AC: 37281 AN: 41504

American (AMR) AF: 0.868 AC: 13266 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2826 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3496 AN: 5166

South Asian (SAS) AF: 0.871 AC: 4202 AN: 4822

European-Finnish (FIN) AF: 0.775 AC: 8190 AN: 10570

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57536 AN: 68020

Other (OTH) AF: 0.838 AC: 1770 AN: 2112

Alfa AF: 0.850 Hom.: 7139

Bravo AF: 0.858

Asia WGS AF: 0.789 AC: 2742 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.36
PhyloP100		0.032
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2676628; hg19: chr9-115369058;