rs7904115

Variant names:

• chr10-24504238-C-T
• rs7904115
• NM_019590.5:c.2001+2693C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019590.5(KIAA1217):​c.2001+2693C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,124 control chromosomes in the GnomAD database, including 7,231 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 0.30 (7231 hom., cov: 33)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658
• 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.2001+2693C>T		intron_variant	Intron 9 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.2001+2693C>T		intron_variant	Intron 9 of 20	1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45879 AN: 152006 Hom.: 7227 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.302 AC: 45895 AN: 152124 Hom.: 7231 Cov.: 33 AF XY: 0.299 AC XY: 22261 AN XY: 74352

African (AFR) AF: 0.380 AC: 15771 AN: 41504

American (AMR) AF: 0.269 AC: 4102 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3472

East Asian (EAS) AF: 0.154 AC: 796 AN: 5182

South Asian (SAS) AF: 0.282 AC: 1357 AN: 4818

European-Finnish (FIN) AF: 0.267 AC: 2815 AN: 10562

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.278 AC: 18883 AN: 68012

Other (OTH) AF: 0.304 AC: 640 AN: 2106

Alfa AF: 0.298 Hom.: 888

Bravo AF: 0.308

Asia WGS AF: 0.236 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.9
DANN	Benign	0.73
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7904115; hg19: chr10-24793167;