rs197383

Positions:

• chr1-111750410-T-C
• chr1-111750410-T-G

Variant summary

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

The NR_125963.1(LOC101928718):​n.379+2688A>G variant causes a intron, non coding transcript 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: LOC101928718 NR_125963.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

Genes affected

(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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928718	NR_125963.1	n.379+2688A>G		intron_variant, non_coding_transcript_variant
INKA2	NM_198926.2	c.12+5291A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412270.1	n.379+2688A>G		intron_variant, non_coding_transcript_variant		1
INKA2	ENST00000444059.2	n.124+5291A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.0957

Gnomad4 ASJ AF: 0.0859

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0812

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.139

Alfa AF: 0.0590 Hom.: 87

Bravo AF: 0.150

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs197383; hg19: chr1-112293032;