rs2802460

Variant names:

• chr10-7787074-T-C
• rs2802460
• NM_012311.4:c.114+746A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012311.4. 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
	KIN	NM_012311.4	MANE Select	c.114+746A>G		intron	N/A	NP_036443.1	O60870-1
	KIN	NR_045609.2		n.174+746A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIN	ENST00000379562.9	TSL:1 MANE Select	c.114+746A>G		intron	N/A	ENSP00000368881.3	O60870-1
	KIN	ENST00000929809.1		c.114+746A>G		intron	N/A	ENSP00000599868.1
	KIN	ENST00000899952.1		c.114+746A>G		intron	N/A	ENSP00000570011.1

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

African (AFR) AF: 0.175 AC: 5593 AN: 32012

American (AMR) AF: 0.314 AC: 4006 AN: 12764

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 976 AN: 3060

East Asian (EAS) AF: 0.211 AC: 1035 AN: 4912

South Asian (SAS) AF: 0.280 AC: 1187 AN: 4242

European-Finnish (FIN) AF: 0.325 AC: 2487 AN: 7654

Middle Eastern (MID) AF: 0.248 AC: 63 AN: 254

European-Non Finnish (NFE) AF: 0.335 AC: 16872 AN: 50400

Other (OTH) AF: 0.272 AC: 439 AN: 1612

Alfa AF: 0.236 Hom.: 13393

Bravo AF: 0.213

Asia WGS AF: 0.245 AC: 796 AN: 3244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.39
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2802460; hg19: chr10-7829037;