X-119141549-A-G

Variant names:

• chrX-119141549-A-G
• rs7892463
• NM_020721.1:c.410+5924T>C

Variant summary

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

The NM_020721.1(KIAA1210):​c.410+5924T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 111,244 control chromosomes in the GnomAD database, including 5,672 homozygotes. There are 12,254 hemizygotes in GnomAD. 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 0.37 (5672 hom., 12254 hem., cov: 24)
• Consequence: KIAA1210 NM_020721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 0 publications found

Genes affected

KIAA1210 (HGNC:29218): (KIAA1210) Predicted to be located in acrosomal vesicle. Predicted to colocalize with basal ectoplasmic specialization. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000306898 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020721.1. 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
	KIAA1210	NM_020721.1		c.410+5924T>C		intron	N/A	NP_065772.1	Q9ULL0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1210	ENST00000402510.2	TSL:5	c.410+5924T>C		intron	N/A	ENSP00000384670.2	Q9ULL0
	ENSG00000306898	ENST00000821878.1		n.-145A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.368 AC: 40878 AN: 111190 Hom.: 5670 Cov.: 24

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.444

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.368 AC: 40899 AN: 111244 Hom.: 5672 Cov.: 24 AF XY: 0.366 AC XY: 12254 AN XY: 33458

African (AFR) AF: 0.225 AC: 6903 AN: 30733

American (AMR) AF: 0.489 AC: 5127 AN: 10476

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1009 AN: 2627

East Asian (EAS) AF: 0.689 AC: 2425 AN: 3522

South Asian (SAS) AF: 0.516 AC: 1366 AN: 2646

European-Finnish (FIN) AF: 0.346 AC: 2039 AN: 5890

Middle Eastern (MID) AF: 0.446 AC: 95 AN: 213

European-Non Finnish (NFE) AF: 0.397 AC: 21043 AN: 52951

Other (OTH) AF: 0.391 AC: 591 AN: 1510

Alfa AF: 0.249 Hom.: 1504

Bravo AF: 0.379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.66
PhyloP100		1.4
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: rs7892463; hg19: chrX-118275512;