1-62238014-G-A

Position:

• chr1-62238014-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.*263C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 376,812 control chromosomes in the GnomAD database, including 696 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.057 (549 hom., cov: 32)
  • Exomes 𝑓: 0.021 (147 hom.)
• Consequence: KANK4 NM_181712.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.259

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=-0.82).
• BP6: Variant 1-62238014-G-A is Benign according to our data. Variant chr1-62238014-G-A is described in ClinVar as [Benign]. Clinvar id is 1233426.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KANK4	NM_181712.5	c.*263C>T		3_prime_UTR_variant	10/10	ENST00000371153.9	NP_859063.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KANK4	ENST00000371153	c.*263C>T		3_prime_UTR_variant	10/10	1	NM_181712.5	ENSP00000360195.4
KANK4	ENST00000354381	c.*263C>T		3_prime_UTR_variant	9/9	2		ENSP00000346352.3
KANK4	ENST00000371150	c.*263C>T		3_prime_UTR_variant	7/7	2		ENSP00000360192.1
KANK4	ENST00000317477	c.*263C>T		3_prime_UTR_variant	4/4	2		ENSP00000321161.4

Frequencies

GnomAD3 genomes AF: 0.0571 AC: 8679 AN: 152098 Hom.: 550 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0256

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0417

GnomAD4 exome AF: 0.0212 AC: 4771 AN: 224596 Hom.: 147 Cov.: 0 AF XY: 0.0209 AC XY: 2383 AN XY: 113868

Gnomad4 AFR exome AF: 0.158

Gnomad4 AMR exome AF: 0.0172

Gnomad4 ASJ exome AF: 0.0255

Gnomad4 EAS exome AF: 0.00190

Gnomad4 SAS exome AF: 0.0135

Gnomad4 FIN exome AF: 0.0242

Gnomad4 NFE exome AF: 0.0154

Gnomad4 OTH exome AF: 0.0264

GnomAD4 genome AF: 0.0571 AC: 8696 AN: 152216 Hom.: 549 Cov.: 32 AF XY: 0.0558 AC XY: 4157 AN XY: 74432

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0264

Gnomad4 ASJ AF: 0.0256

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0172

Gnomad4 FIN AF: 0.0289

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0355 Hom.: 122

Bravo AF: 0.0607

Asia WGS AF: 0.0110 AC: 38 AN: 3478

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

Dec 25, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.67

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: rs17123220; hg19: chr1-62703686;