chr6-89490294-C-T

Position:

• chr6-89490294-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.-144+56919C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 152,296 control chromosomes in the GnomAD database, including 561 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 0.079 (561 hom., cov: 32)
• Consequence: ANKRD6 NM_001242809.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD6	NM_001242809.2	c.-144+56919C>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.-144+56919C>T		intron_variant		1	NM_001242809.2	ENSP00000345767	A1

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11935 AN: 152176 Hom.: 557 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0585

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0786 AC: 11975 AN: 152296 Hom.: 561 Cov.: 32 AF XY: 0.0792 AC XY: 5898 AN XY: 74470

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0560

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.0280

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0544

Gnomad4 NFE AF: 0.0585

Gnomad4 OTH AF: 0.0827

Alfa AF: 0.0716 Hom.: 123

Bravo AF: 0.0786

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.3
DANN	Benign	0.77

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: rs6934871; hg19: chr6-90200013;