rs3818672

Variant names:

• chr10-24494464-C-A
• rs3818672
• NM_019590.5:c.1680-36C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-24494464-C-A
• chr10-24494464-C-G

Variant summary

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

The NM_019590.5(KIAA1217):​c.1680-36C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,553,722 control chromosomes in the GnomAD database, including 38,737 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 0.25 (5381 hom., cov: 32)
  • Exomes 𝑓: 0.21 (33356 hom.)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44
• Publications: 6 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=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 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.1680-36C>A		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.1680-683C>A		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.1680-683C>A		intron	N/A	NP_001269697.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	ENST00000376454.8	TSL:1 MANE Select	c.1680-36C>A		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376451.4	TSL:1	c.834-683C>A		intron	N/A	ENSP00000365634.2
	KIAA1217	ENST00000376452.7	TSL:1	c.1680-683C>A		intron	N/A	ENSP00000365635.3

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37760 AN: 151658 Hom.: 5364 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.264

GnomAD2 exomes AF: 0.238 AC: 59307 AN: 249068 AF XY: 0.240

Gnomad AFR exome AF: 0.365

Gnomad AMR exome AF: 0.243

Gnomad ASJ exome AF: 0.208

Gnomad EAS exome AF: 0.355

Gnomad FIN exome AF: 0.129

Gnomad NFE exome AF: 0.187

Gnomad OTH exome AF: 0.231

GnomAD4 exome AF: 0.208 AC: 291256 AN: 1401944 Hom.: 33356 Cov.: 22 AF XY: 0.212 AC XY: 148977 AN XY: 701138

African (AFR) AF: 0.371 AC: 11924 AN: 32144

American (AMR) AF: 0.241 AC: 10612 AN: 44080

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 5241 AN: 25780

East Asian (EAS) AF: 0.358 AC: 14076 AN: 39354

South Asian (SAS) AF: 0.370 AC: 31339 AN: 84684

European-Finnish (FIN) AF: 0.135 AC: 7158 AN: 53032

Middle Eastern (MID) AF: 0.332 AC: 1877 AN: 5656

European-Non Finnish (NFE) AF: 0.185 AC: 195355 AN: 1058766

Other (OTH) AF: 0.234 AC: 13674 AN: 58448

GnomAD4 genome AF: 0.249 AC: 37817 AN: 151778 Hom.: 5381 Cov.: 32 AF XY: 0.247 AC XY: 18358 AN XY: 74198

African (AFR) AF: 0.363 AC: 14972 AN: 41296

American (AMR) AF: 0.239 AC: 3649 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 712 AN: 3470

East Asian (EAS) AF: 0.348 AC: 1788 AN: 5138

South Asian (SAS) AF: 0.380 AC: 1820 AN: 4784

European-Finnish (FIN) AF: 0.125 AC: 1316 AN: 10558

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12810 AN: 67946

Other (OTH) AF: 0.270 AC: 568 AN: 2106

Alfa AF: 0.217 Hom.: 1429

Bravo AF: 0.264

Asia WGS AF: 0.388 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	14
DANN	Benign	0.61
PhyloP100		3.4
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: rs3818672; hg19: chr10-24783393; COSMIC: COSV56817428; COSMIC: COSV56817428;