rs7072944

Variant names:

• chr10-24222234-T-C
• rs7072944
• NM_019590.5:c.354+2325T>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.354+2325T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,032 control chromosomes in the GnomAD database, including 24,441 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 0.57 (24441 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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.354+2325T>C		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.354+2325T>C		intron	N/A	NP_001269696.1	Q5T5P2-10
	KIAA1217	NM_001282768.2		c.354+2325T>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.354+2325T>C		intron	N/A	ENSP00000365637.3	Q5T5P2-1
	KIAA1217	ENST00000376452.7	TSL:1	c.354+2325T>C		intron	N/A	ENSP00000365635.3	Q5T5P2-10
	KIAA1217	ENST00000458595.5	TSL:1	c.354+2325T>C		intron	N/A	ENSP00000392625.1	Q5T5P2-7

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85990 AN: 151914 Hom.: 24417 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.566 AC: 86071 AN: 152032 Hom.: 24441 Cov.: 32 AF XY: 0.562 AC XY: 41782 AN XY: 74304

African (AFR) AF: 0.611 AC: 25346 AN: 41478

American (AMR) AF: 0.525 AC: 8028 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1993 AN: 3464

East Asian (EAS) AF: 0.636 AC: 3278 AN: 5156

South Asian (SAS) AF: 0.563 AC: 2710 AN: 4810

European-Finnish (FIN) AF: 0.510 AC: 5387 AN: 10568

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37360 AN: 67960

Other (OTH) AF: 0.607 AC: 1281 AN: 2112

Alfa AF: 0.553 Hom.: 3073

Bravo AF: 0.571

Asia WGS AF: 0.606 AC: 2109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		0.21
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: rs7072944; hg19: chr10-24511163;