chr1-62247327-TG-T

Position:

• chr1-62247327-TG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_181712.5(KANK4):​c.2883+144delC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 611,920 control chromosomes in the GnomAD database, including 55,593 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.43 (13914 hom., cov: 0)
  • Exomes 𝑓: 0.41 (41679 hom.)
• Consequence: KANK4 NM_181712.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.112

Genes affected

KANK4 (HGNC:27263): (KN motif and ankyrin repeat domains 4) Predicted to be involved in negative regulation of actin filament polymerization. Located in cytosol and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-62247327-TG-T is Benign according to our data. Variant chr1-62247327-TG-T is described in ClinVar as [Benign]. Clinvar id is 1279369.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KANK4	NM_181712.5	c.2883+144delC		intron_variant		ENST00000371153.9	NP_859063.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KANK4	ENST00000371153.9	c.2883+144delC		intron_variant		1	NM_181712.5	ENSP00000360195.4
KANK4	ENST00000354381.3	c.999+144delC		intron_variant		2		ENSP00000346352.3
KANK4	ENST00000371150.5	c.951+144delC		intron_variant		2		ENSP00000360192.1
KANK4	ENST00000317477.8	c.297+144delC		intron_variant		2		ENSP00000321161.4

Frequencies

GnomAD3 genomes AF: 0.431 AC: 63552 AN: 147502 Hom.: 13896 Cov.: 0

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.409

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.417

GnomAD4 exome AF: 0.413 AC: 191862 AN: 464306 Hom.: 41679 AF XY: 0.409 AC XY: 100046 AN XY: 244392

Gnomad4 AFR exome AF: 0.431

Gnomad4 AMR exome AF: 0.387

Gnomad4 ASJ exome AF: 0.421

Gnomad4 EAS exome AF: 0.194

Gnomad4 SAS exome AF: 0.324

Gnomad4 FIN exome AF: 0.478

Gnomad4 NFE exome AF: 0.445

Gnomad4 OTH exome AF: 0.416

GnomAD4 genome AF: 0.431 AC: 63620 AN: 147614 Hom.: 13914 Cov.: 0 AF XY: 0.429 AC XY: 30840 AN XY: 71806

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.412

Asia WGS AF: 0.247 AC: 855 AN: 3458

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs111297754; hg19: chr1-62712999;