1-62261924-T-C

Variant names:

• chr1-62261924-T-C
• rs2765241
• NM_181712.5:c.2539+1168A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181712.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KANK4	NM_181712.5	MANE Select	c.2539+1168A>G		intron	N/A	NP_859063.3
	KANK4	NM_001320269.2		c.655+1168A>G		intron	N/A	NP_001307198.1	Q5T7N3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KANK4	ENST00000371153.9	TSL:1 MANE Select	c.2539+1168A>G		intron	N/A	ENSP00000360195.4	Q5T7N3-1
	KANK4	ENST00000880984.1		c.2539+1168A>G		intron	N/A	ENSP00000551043.1
	KANK4	ENST00000880985.1		c.2539+1168A>G		intron	N/A	ENSP00000551044.1

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

African (AFR) AF: 0.767 AC: 31775 AN: 41440

American (AMR) AF: 0.812 AC: 12418 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2488 AN: 3472

East Asian (EAS) AF: 0.835 AC: 4299 AN: 5148

South Asian (SAS) AF: 0.789 AC: 3795 AN: 4812

European-Finnish (FIN) AF: 0.851 AC: 9000 AN: 10582

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50617 AN: 67972

Other (OTH) AF: 0.752 AC: 1588 AN: 2112

Alfa AF: 0.747 Hom.: 178988

Bravo AF: 0.766

Asia WGS AF: 0.820 AC: 2851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.3
DANN	Benign	0.72
PhyloP100		-0.062
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2765241; hg19: chr1-62727596;