rs5909594

Variant names:

• chrX-119141353-G-A
• rs5909594
• NM_020721.1:c.410+6120C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-119141353-G-A
• chrX-119141353-G-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_020721.1(KIAA1210):​c.410+6120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.54 (11583 hom., 17486 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: KIAA1210 NM_020721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 2 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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1210	NM_020721.1	c.410+6120C>T		intron_variant	Intron 2 of 13		NP_065772.1
KIAA1210	XM_017029688.3	c.35+9584C>T		intron_variant	Intron 1 of 11		XP_016885177.1
KIAA1210	XM_017029689.3	c.35+9584C>T		intron_variant	Intron 1 of 10		XP_016885178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1210	ENST00000402510.2	c.410+6120C>T		intron_variant	Intron 2 of 13	5		ENSP00000384670.2

Frequencies

GnomAD3 genomes AF: 0.539 AC: 59491 AN: 110316 Hom.: 11584 Cov.: 23

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.524

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.546

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.539 AC: 59498 AN: 110369 Hom.: 11583 Cov.: 23 AF XY: 0.535 AC XY: 17486 AN XY: 32671

African (AFR) AF: 0.464 AC: 14088 AN: 30330

American (AMR) AF: 0.473 AC: 4919 AN: 10404

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 1625 AN: 2636

East Asian (EAS) AF: 0.306 AC: 1071 AN: 3496

South Asian (SAS) AF: 0.460 AC: 1194 AN: 2596

European-Finnish (FIN) AF: 0.637 AC: 3690 AN: 5790

Middle Eastern (MID) AF: 0.521 AC: 110 AN: 211

European-Non Finnish (NFE) AF: 0.600 AC: 31612 AN: 52727

Other (OTH) AF: 0.543 AC: 821 AN: 1513

Alfa AF: 0.562 Hom.: 21122

Bravo AF: 0.522

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.62
PhyloP100		-0.077
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: rs5909594; hg19: chrX-118275316;