rs6934871

Variant names:

• chr6-89490294-C-T
• rs6934871
• NM_001242809.2:c.-144+56919C>T

Variant summary

Our verdict is Benign. The variant received -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
• 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242809.2. 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.-144+56919C>T		intron	N/A	NP_001229738.1
	ANKRD6	NM_014942.4		c.-144+56919C>T		intron	N/A	NP_055757.3
	ANKRD6	NM_001242813.1		c.-144+56919C>T		intron	N/A	NP_001229742.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD6	ENST00000339746.9	TSL:1 MANE Select	c.-144+56919C>T		intron	N/A	ENSP00000345767.4
	ANKRD6	ENST00000447838.6	TSL:1	c.-144+56919C>T		intron	N/A	ENSP00000396771.2
	ANKRD6	ENST00000369408.9	TSL:1	c.-144+56919C>T		intron	N/A	ENSP00000358416.5

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

African (AFR) AF: 0.122 AC: 5049 AN: 41554

American (AMR) AF: 0.0560 AC: 857 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3470

East Asian (EAS) AF: 0.0280 AC: 145 AN: 5186

South Asian (SAS) AF: 0.145 AC: 702 AN: 4828

European-Finnish (FIN) AF: 0.0544 AC: 577 AN: 10610

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0585 AC: 3982 AN: 68022

Other (OTH) AF: 0.0827 AC: 175 AN: 2116

Alfa AF: 0.0727 Hom.: 132

Bravo AF: 0.0786

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.3
DANN	Benign	0.77
PhyloP100		0.27
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: rs6934871; hg19: chr6-90200013;