1-111750410-T-C

Variant names:

• chr1-111750410-T-C
• rs197383
• ENST00000412270.1:n.379+2688A>G

Variant summary

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

The NM_198926.2(INKA2):​c.12+5291A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,220 control chromosomes in the GnomAD database, including 2,109 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 0.15 (2109 hom., cov: 33)
• Consequence: INKA2 NM_198926.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 7 publications found

Genes affected

ENSG00000284830 (HGNC:):

INKA2 (HGNC:28045): (inka box actin regulator 2) Enables protein kinase binding activity. Predicted to be involved in negative regulation of catalytic activity. Located in nucleoplasm. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198926.2. 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
	INKA2	NM_198926.2		c.12+5291A>G		intron	N/A	NP_945120.1
	LOC101928718	NR_125963.1		n.379+2688A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284830	ENST00000412270.1	TSL:1	n.379+2688A>G		intron	N/A
	INKA2	ENST00000444059.2	TSL:1	n.124+5291A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22716 AN: 152102 Hom.: 2113 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0960

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.0809

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.149 AC: 22735 AN: 152220 Hom.: 2109 Cov.: 33 AF XY: 0.146 AC XY: 10875 AN XY: 74424

African (AFR) AF: 0.261 AC: 10844 AN: 41492

American (AMR) AF: 0.0957 AC: 1464 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 298 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5192

South Asian (SAS) AF: 0.0812 AC: 392 AN: 4828

European-Finnish (FIN) AF: 0.128 AC: 1354 AN: 10604

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7927 AN: 68014

Other (OTH) AF: 0.139 AC: 293 AN: 2112

Alfa AF: 0.0651 Hom.: 111

Bravo AF: 0.150

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.73
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs197383; hg19: chr1-112293032;