rs11255367

Positions:

• chr10-7787055-G-A

Variant summary

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

The NM_012311.4(KIN):​c.114+765C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 146,352 control chromosomes in the GnomAD database, including 1,066 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 0.10 (1066 hom., cov: 32)
• Consequence: KIN NM_012311.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIN	NM_012311.4	c.114+765C>T		intron_variant		ENST00000379562.9	NP_036443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIN	ENST00000379562.9	c.114+765C>T		intron_variant		1	NM_012311.4	ENSP00000368881	P1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15086 AN: 146244 Hom.: 1066 Cov.: 32

Gnomad AFR AF: 0.0228

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.103 AC: 15091 AN: 146352 Hom.: 1066 Cov.: 32 AF XY: 0.108 AC XY: 7691 AN XY: 71358

Gnomad4 AFR AF: 0.0228

Gnomad4 AMR AF: 0.0780

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.110

Alfa AF: 0.115 Hom.: 1557

Bravo AF: 0.0850

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.50

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: rs11255367; hg19: chr10-7829018;