6-89631015-G-A

Position:

• chr6-89631015-G-A

Variant summary

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

The NM_001242809.2(ANKRD6):​c.*11G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 1,492,234 control chromosomes in the GnomAD database, including 23,351 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 0.17 (2369 hom., cov: 33)
  • Exomes 𝑓: 0.18 (20982 hom.)
• Consequence: ANKRD6 NM_001242809.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

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]

ANKRD6 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD6	NM_001242809.2	c.*11G>A		3_prime_UTR_variant	16/16	ENST00000339746.9	NP_001229738.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD6	ENST00000339746.9	c.*11G>A		3_prime_UTR_variant	16/16	1	NM_001242809.2	ENSP00000345767.4

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26476 AN: 152050 Hom.: 2367 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.185

GnomAD3 exomes AF: 0.176 AC: 19092 AN: 108432 Hom.: 1718 AF XY: 0.175 AC XY: 9929 AN XY: 56650

Gnomad AFR exome AF: 0.182

Gnomad AMR exome AF: 0.144

Gnomad ASJ exome AF: 0.223

Gnomad EAS exome AF: 0.214

Gnomad SAS exome AF: 0.107

Gnomad FIN exome AF: 0.185

Gnomad NFE exome AF: 0.190

Gnomad OTH exome AF: 0.172

GnomAD4 exome AF: 0.175 AC: 234751 AN: 1340066 Hom.: 20982 Cov.: 34 AF XY: 0.174 AC XY: 114388 AN XY: 656506

Gnomad4 AFR exome AF: 0.170

Gnomad4 AMR exome AF: 0.137

Gnomad4 ASJ exome AF: 0.213

Gnomad4 EAS exome AF: 0.194

Gnomad4 SAS exome AF: 0.109

Gnomad4 FIN exome AF: 0.173

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.180

GnomAD4 genome AF: 0.174 AC: 26488 AN: 152168 Hom.: 2369 Cov.: 33 AF XY: 0.175 AC XY: 13033 AN XY: 74392

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.182

Alfa AF: 0.175 Hom.: 667

Bravo AF: 0.173

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.60
DANN	Benign	0.49

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: rs9344950; hg19: chr6-90340734;