rs220361

Variant names:

• chr10-24284050-T-C
• rs220361
• NM_019590.5:c.354+64141T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-24284050-T-C
• chr10-24284050-T-G

Variant summary

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

The ENST00000376454.8(KIAA1217):​c.354+64141T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,552 control chromosomes in the GnomAD database, including 19,925 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 0.50 (19925 hom., cov: 29)
• Consequence: KIAA1217 ENST00000376454.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000376454.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	NM_019590.5	MANE Select	c.354+64141T>C		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.354+64141T>C		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.354+64141T>C		intron	N/A	NP_001269697.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	ENST00000376454.8	TSL:1 MANE Select	c.354+64141T>C		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376452.7	TSL:1	c.354+64141T>C		intron	N/A	ENSP00000365635.3
	KIAA1217	ENST00000458595.5	TSL:1	c.354+64141T>C		intron	N/A	ENSP00000392625.1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76018 AN: 151436 Hom.: 19924 Cov.: 29

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.502 AC: 76050 AN: 151552 Hom.: 19925 Cov.: 29 AF XY: 0.497 AC XY: 36821 AN XY: 74076

African (AFR) AF: 0.592 AC: 24460 AN: 41320

American (AMR) AF: 0.393 AC: 5982 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3468

East Asian (EAS) AF: 0.149 AC: 762 AN: 5126

South Asian (SAS) AF: 0.257 AC: 1226 AN: 4770

European-Finnish (FIN) AF: 0.581 AC: 6095 AN: 10488

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34393 AN: 67850

Other (OTH) AF: 0.466 AC: 978 AN: 2100

Alfa AF: 0.404 Hom.: 1173

Bravo AF: 0.497

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.47
PhyloP100		-0.79
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs220361; hg19: chr10-24572979; COSMIC: COSV64601871;