rs2802460

chr10-7787074-T-C

Variant summary

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

The NM_012311.4(KIN):c.114+746A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 117,498 control chromosomes in the GnomAD database, including 3,671 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 0.28 (3671 hom., cov: 29)
• Consequence: KIN NM_012311.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

Genes affected

KIN (HGNC:6327): (Kin17 DNA and RNA binding protein) The protein encoded by this gene is a nuclear protein that forms intranuclear foci during proliferation and is redistributed in the nucleoplasm during the cell cycle. Short-wave ultraviolet light provokes the relocalization of the protein, suggesting its participation in the cellular response to DNA damage. Originally selected based on protein-binding with RecA antibodies, the mouse protein presents a limited similarity with a functional domain of the bacterial RecA protein, a characteristic shared by this human ortholog. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIN	NM_012311.4	c.114+746A>G		intron_variant		ENST00000379562.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIN	ENST00000379562.9	c.114+746A>G		intron_variant		1	NM_012311.4	P1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 32818 AN: 117428 Hom.: 3671 Cov.: 29

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.254

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.279 AC: 32824 AN: 117498 Hom.: 3671 Cov.: 29 AF XY: 0.280 AC XY: 16169 AN XY: 57660

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.272

Alfa AF: 0.242 Hom.: 9008

Bravo AF: 0.213

Asia WGS AF: 0.245 AC: 796 AN: 3244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.10
Dann	Benign	0.39

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: rs2802460; hg19: chr10-7829037;