6-89611439-C-T

Position:

• chr6-89611439-C-T

Variant summary

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

The NM_001242809.2(ANKRD6):​c.418-833C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,278 control chromosomes in the GnomAD database, including 61,778 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 0.90 (61778 hom., cov: 33)
• Consequence: ANKRD6 NM_001242809.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239

Genes affected

ANKRD6 (HGNC:17280): (ankyrin repeat domain 6) Predicted to be involved in negative regulation of canonical Wnt signaling pathway and positive regulation of JNK cascade. Predicted to act upstream of or within positive regulation of Wnt signaling pathway, planar cell polarity pathway. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

LYRM2 (HGNC:25229): (LYR motif containing 2)

ANKRD6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD6	NM_001242809.2	c.418-833C>T		intron_variant		ENST00000339746.9	NP_001229738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD6	ENST00000339746.9	c.418-833C>T		intron_variant		1	NM_001242809.2	ENSP00000345767.4

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136746 AN: 152160 Hom.: 61714 Cov.: 33

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.899 AC: 136867 AN: 152278 Hom.: 61778 Cov.: 33 AF XY: 0.902 AC XY: 67156 AN XY: 74456

Gnomad4 AFR AF: 0.973

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.892

Alfa AF: 0.873 Hom.: 7198

Bravo AF: 0.907

Asia WGS AF: 0.951 AC: 3308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.24

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: rs1179900; hg19: chr6-90321158;