rs2676628

chr9-112606778-G-Achr9-112606778-G-Cchr9-112606778-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

KIAA1958 (HGNC:23427): (KIAA1958)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1958	NM_133465.4	c.1171+31527G>A		intron_variant		ENST00000337530.11
KIAA1958	NM_001287036.2	c.1172-11093G>A		intron_variant
KIAA1958	NM_001287038.2	c.1171+31527G>A		intron_variant
KIAA1958	XM_011518311.3	c.1172-11093G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1958	ENST00000337530.11	c.1171+31527G>A		intron_variant		1	NM_133465.4	P4
KIAA1958	ENST00000536272.5	c.1172-11093G>A		intron_variant		1		A1
KIAA1958	ENST00000374244.3	c.1172-11093G>A		intron_variant		5

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

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.838

Alfa AF: 0.849 Hom.: 6834

Bravo AF: 0.858

Asia WGS AF: 0.789 AC: 2742 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.7
Dann	Benign	0.36

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

Publications

LitVar

Other links and lift over

dbSNP: rs2676628; hg19: chr9-115369058;