6-89611439-C-T

Variant names:

• chr6-89611439-C-T
• rs1179900
• NM_001242809.2:c.418-833C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000339746.9(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 ENST00000339746.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 2 publications found

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)

LOC124901359 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000339746.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD6	NM_001242809.2	MANE Select	c.418-833C>T		intron	N/A	NP_001229738.1
	ANKRD6	NM_001242811.1		c.418-833C>T		intron	N/A	NP_001229740.1
	ANKRD6	NM_014942.4		c.418-833C>T		intron	N/A	NP_055757.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD6	ENST00000339746.9	TSL:1 MANE Select	c.418-833C>T		intron	N/A	ENSP00000345767.4
	ANKRD6	ENST00000447838.6	TSL:1	c.418-833C>T		intron	N/A	ENSP00000396771.2
	ANKRD6	ENST00000369408.9	TSL:1	c.418-833C>T		intron	N/A	ENSP00000358416.5

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

African (AFR) AF: 0.973 AC: 40433 AN: 41562

American (AMR) AF: 0.932 AC: 14263 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3011 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5176 AN: 5182

South Asian (SAS) AF: 0.886 AC: 4274 AN: 4824

European-Finnish (FIN) AF: 0.867 AC: 9196 AN: 10612

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57613 AN: 68006

Other (OTH) AF: 0.892 AC: 1883 AN: 2112

Alfa AF: 0.877 Hom.: 7563

Bravo AF: 0.907

Asia WGS AF: 0.951 AC: 3308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.24
PhyloP100		-0.24
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: rs1179900; hg19: chr6-90321158;