chr1-62261924-T-C

Position:

• chr1-62261924-T-C

Variant summary

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

The NM_181712.5(KANK4):​c.2539+1168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,028 control chromosomes in the GnomAD database, including 44,975 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 0.77 (44975 hom., cov: 31)
• Consequence: KANK4 NM_181712.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KANK4	NM_181712.5	c.2539+1168A>G		intron_variant		ENST00000371153.9	NP_859063.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KANK4	ENST00000371153.9	c.2539+1168A>G		intron_variant		1	NM_181712.5	ENSP00000360195	P1
KANK4	ENST00000317477.8	c.-48+1168A>G		intron_variant		2		ENSP00000321161
KANK4	ENST00000354381.3	c.655+1168A>G		intron_variant		2		ENSP00000346352
KANK4	ENST00000371150.5	c.607+1168A>G		intron_variant		2		ENSP00000360192

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116683 AN: 151908 Hom.: 44920 Cov.: 31

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.768 AC: 116802 AN: 152028 Hom.: 44975 Cov.: 31 AF XY: 0.776 AC XY: 57630 AN XY: 74296

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.752

Alfa AF: 0.744 Hom.: 85219

Bravo AF: 0.766

Asia WGS AF: 0.820 AC: 2851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.3
DANN	Benign	0.72

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: rs2765241; hg19: chr1-62727596;