chr10-24409406-A-C

Variant names:

• chr10-24409406-A-C
• rs12412510
• NM_019590.5:c.554-23589A>C

Variant summary

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

The NM_019590.5(KIAA1217):​c.554-23589A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0536 in 152,210 control chromosomes in the GnomAD database, including 219 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 0.054 (219 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 0 publications found

Genes affected

KIAA1217 (HGNC:25428): (KIAA1217) Predicted to be involved in embryonic skeletal system development. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019590.5. 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
	KIAA1217	NM_019590.5	MANE Select	c.554-23589A>C		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.554-23589A>C		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.554-23589A>C		intron	N/A	NP_001269697.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	ENST00000376454.8	TSL:1 MANE Select	c.554-23589A>C		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376452.7	TSL:1	c.554-23589A>C		intron	N/A	ENSP00000365635.3
	KIAA1217	ENST00000458595.5	TSL:1	c.554-23589A>C		intron	N/A	ENSP00000392625.1

Frequencies

GnomAD3 genomes AF: 0.0536 AC: 8157 AN: 152092 Hom.: 219 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0551

Gnomad SAS AF: 0.0417

Gnomad FIN AF: 0.0370

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0536 AC: 8160 AN: 152210 Hom.: 219 Cov.: 32 AF XY: 0.0523 AC XY: 3889 AN XY: 74424

African (AFR) AF: 0.0473 AC: 1966 AN: 41534

American (AMR) AF: 0.0714 AC: 1092 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3472

East Asian (EAS) AF: 0.0548 AC: 284 AN: 5178

South Asian (SAS) AF: 0.0417 AC: 201 AN: 4818

European-Finnish (FIN) AF: 0.0370 AC: 392 AN: 10602

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0574 AC: 3902 AN: 68000

Other (OTH) AF: 0.0492 AC: 104 AN: 2112

Alfa AF: 0.0153 Hom.: 8

Bravo AF: 0.0568

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.57
PhyloP100		0.0050
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: rs12412510; hg19: chr10-24698335;