NM_019590.5:c.752+1444A>C

Variant names:

• chr10-24434637-A-C
• rs1331291
• NM_019590.5:c.752+1444A>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.752+1444A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,196 control chromosomes in the GnomAD database, including 3,122 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 0.19 (3122 hom., cov: 33)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20
• Publications: 2 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]

LOC124902395 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 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.752+1444A>C		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.752+1444A>C		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.752+1444A>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.752+1444A>C		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376452.7	TSL:1	c.752+1444A>C		intron	N/A	ENSP00000365635.3
	KIAA1217	ENST00000458595.5	TSL:1	c.752+1444A>C		intron	N/A	ENSP00000392625.1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28629 AN: 152078 Hom.: 3118 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.188 AC: 28657 AN: 152196 Hom.: 3122 Cov.: 33 AF XY: 0.193 AC XY: 14396 AN XY: 74400

African (AFR) AF: 0.236 AC: 9787 AN: 41536

American (AMR) AF: 0.219 AC: 3346 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3468

East Asian (EAS) AF: 0.367 AC: 1894 AN: 5166

South Asian (SAS) AF: 0.370 AC: 1784 AN: 4816

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10614

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9538 AN: 67992

Other (OTH) AF: 0.212 AC: 448 AN: 2112

Alfa AF: 0.154 Hom.: 3087

Bravo AF: 0.194

Asia WGS AF: 0.380 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.4
DANN	Benign	0.75
PhyloP100		2.2
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: rs1331291; hg19: chr10-24723566;