NM_019590.5:c.554-1826T>G

Variant names:

• chr10-24431169-T-G
• rs7087652
• NM_019590.5:c.554-1826T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019590.5(KIAA1217):​c.554-1826T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,994 control chromosomes in the GnomAD database, including 7,412 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 0.31 (7412 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.554-1826T>G		intron_variant	Intron 3 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.554-1826T>G		intron_variant	Intron 3 of 20	1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46901 AN: 151874 Hom.: 7411 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.309 AC: 46923 AN: 151994 Hom.: 7412 Cov.: 32 AF XY: 0.311 AC XY: 23066 AN XY: 74276

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.266

Alfa AF: 0.294 Hom.: 9298

Bravo AF: 0.299

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.78

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

Publications

LitVar

Other links and lift over

dbSNP: rs7087652; hg19: chr10-24720098; COSMIC: COSV64612045;