rs10508672

Variant names:

• chr10-24245506-G-A
• rs10508672
• NM_019590.5:c.354+25597G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-24245506-G-A
• chr10-24245506-G-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+25597G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,150 control chromosomes in the GnomAD database, including 1,985 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 0.12 (1985 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• 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 = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.354+25597G>A		intron_variant	Intron 2 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.354+25597G>A		intron_variant	Intron 2 of 20	1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18657 AN: 152032 Hom.: 1965 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0355

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0355

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.123 AC: 18719 AN: 152150 Hom.: 1985 Cov.: 32 AF XY: 0.127 AC XY: 9445 AN XY: 74384

African (AFR) AF: 0.252 AC: 10469 AN: 41484

American (AMR) AF: 0.207 AC: 3161 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0355 AC: 123 AN: 3468

East Asian (EAS) AF: 0.193 AC: 998 AN: 5160

South Asian (SAS) AF: 0.153 AC: 735 AN: 4818

European-Finnish (FIN) AF: 0.0475 AC: 504 AN: 10606

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0355 AC: 2414 AN: 68012

Other (OTH) AF: 0.105 AC: 223 AN: 2114

Alfa AF: 0.0836 Hom.: 348

Bravo AF: 0.141

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.58
PhyloP100		-0.49
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: rs10508672; hg19: chr10-24534435;