1-62238654-G-A

Position:

• chr1-62238654-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_181712.5(KANK4):​c.2884-273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 134,056 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.019 (68 hom., cov: 30)
• Consequence: KANK4 NM_181712.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.802

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 1-62238654-G-A is Benign according to our data. Variant chr1-62238654-G-A is described in ClinVar as [Benign]. Clinvar id is 1279706.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KANK4	NM_181712.5	c.2884-273C>T		intron_variant		ENST00000371153.9	NP_859063.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KANK4	ENST00000371153.9	c.2884-273C>T		intron_variant		1	NM_181712.5	ENSP00000360195.4
KANK4	ENST00000354381.3	c.1000-273C>T		intron_variant		2		ENSP00000346352.3
KANK4	ENST00000371150.5	c.952-273C>T		intron_variant		2		ENSP00000360192.1
KANK4	ENST00000317477.8	c.298-273C>T		intron_variant		2		ENSP00000321161.4

Frequencies

GnomAD3 genomes AF: 0.0190 AC: 2542 AN: 133962 Hom.: 68 Cov.: 30

Gnomad AFR AF: 0.0621

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00726

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000233

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000216

Gnomad OTH AF: 0.0147

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

GnomAD4 genome AF: 0.0190 AC: 2551 AN: 134056 Hom.: 68 Cov.: 30 AF XY: 0.0188 AC XY: 1211 AN XY: 64322

Gnomad4 AFR AF: 0.0621

Gnomad4 AMR AF: 0.00726

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000234

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000216

Gnomad4 OTH AF: 0.0146

Alfa AF: 0.0148 Hom.: 4

Bravo AF: 0.0203

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

Apr 26, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.80

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: rs141306557; hg19: chr1-62704326;