rs16838917

chr2-202170700-G-A

Variant summary

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

The NM_001277372.4(KIAA2012):c.2119+5344G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0623 in 152,240 control chromosomes in the GnomAD database, including 381 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 0.062 (381 hom., cov: 32)
• Consequence: KIAA2012 NM_001277372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

Genes affected

KIAA2012 (HGNC:51250): (KIAA2012)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA2012	NM_001277372.4	c.2119+5344G>A		intron_variant		ENST00000498697.3
KIAA2012	NM_001367720.2	c.2116+5344G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA2012	ENST00000498697.3	c.2119+5344G>A		intron_variant		5	NM_001277372.4	P1
KIAA2012	ENST00000469462.1	n.3004+5344G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0623 AC: 9482 AN: 152122 Hom.: 380 Cov.: 32

Gnomad AFR AF: 0.0374

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.0676

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00288

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0796

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0623 AC: 9482 AN: 152240 Hom.: 381 Cov.: 32 AF XY: 0.0597 AC XY: 4444 AN XY: 74444

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.0675

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.0860

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.0796

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.0693 Hom.: 112

Bravo AF: 0.0649

Asia WGS AF: 0.0460 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.4
Dann	Benign	0.40

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: rs16838917; hg19: chr2-203035423;