10-24378162-T-C

Variant names:

• chr10-24378162-T-C
• rs11014072
• NM_019590.5:c.355-2707T>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.355-2707T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,064 control chromosomes in the GnomAD database, including 17,814 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 0.47 (17814 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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.355-2707T>C		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.355-2707T>C		intron	N/A	NP_001269696.1	Q5T5P2-10
	KIAA1217	NM_001282768.2		c.355-2707T>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.355-2707T>C		intron	N/A	ENSP00000365637.3	Q5T5P2-1
	KIAA1217	ENST00000376452.7	TSL:1	c.355-2707T>C		intron	N/A	ENSP00000365635.3	Q5T5P2-10
	KIAA1217	ENST00000458595.5	TSL:1	c.355-2707T>C		intron	N/A	ENSP00000392625.1	Q5T5P2-7

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70917 AN: 151946 Hom.: 17777 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.467 AC: 71010 AN: 152064 Hom.: 17814 Cov.: 32 AF XY: 0.463 AC XY: 34421 AN XY: 74298

African (AFR) AF: 0.658 AC: 27292 AN: 41472

American (AMR) AF: 0.395 AC: 6035 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1623 AN: 3472

East Asian (EAS) AF: 0.441 AC: 2281 AN: 5176

South Asian (SAS) AF: 0.508 AC: 2439 AN: 4802

European-Finnish (FIN) AF: 0.323 AC: 3413 AN: 10560

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26492 AN: 67978

Other (OTH) AF: 0.460 AC: 971 AN: 2112

Alfa AF: 0.406 Hom.: 21773

Bravo AF: 0.477

Asia WGS AF: 0.482 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.52
PhyloP100		-1.6
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: rs11014072; hg19: chr10-24667091;