10-24377897-T-C

Variant names:

• chr10-24377897-T-C
• rs16924711
• NM_019590.5:c.355-2972T>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.355-2972T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,072 control chromosomes in the GnomAD database, including 1,380 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 0.13 (1380 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• 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 (SAS) allele frequency at 95% confidence interval = 0.297 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	NM_019590.5	MANE Select	c.355-2972T>C		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.355-2972T>C		intron	N/A	NP_001269696.1	Q5T5P2-10
	KIAA1217	NM_001282768.2		c.355-2972T>C		intron	N/A	NP_001269697.1	Q5T5P2-7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	ENST00000376454.8	TSL:1 MANE Select	c.355-2972T>C		intron	N/A	ENSP00000365637.3	Q5T5P2-1
	KIAA1217	ENST00000376452.7	TSL:1	c.355-2972T>C		intron	N/A	ENSP00000365635.3	Q5T5P2-10
	KIAA1217	ENST00000458595.5	TSL:1	c.355-2972T>C		intron	N/A	ENSP00000392625.1	Q5T5P2-7

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19294 AN: 151954 Hom.: 1362 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0780

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.0681

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.127 AC: 19348 AN: 152072 Hom.: 1380 Cov.: 32 AF XY: 0.130 AC XY: 9663 AN XY: 74340

African (AFR) AF: 0.111 AC: 4612 AN: 41500

American (AMR) AF: 0.156 AC: 2388 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3466

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5166

South Asian (SAS) AF: 0.310 AC: 1492 AN: 4808

European-Finnish (FIN) AF: 0.0681 AC: 720 AN: 10574

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8014 AN: 67972

Other (OTH) AF: 0.160 AC: 337 AN: 2108

Alfa AF: 0.123 Hom.: 1495

Bravo AF: 0.129

Asia WGS AF: 0.254 AC: 883 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	0.20
DANN	Benign	0.28
PhyloP100		-2.0
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: rs16924711; hg19: chr10-24666826;