rs9344950

Variant names:

• chr6-89631015-G-A
• rs9344950
• NM_001242809.2:c.*11G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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)

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD6	NM_001242809.2	MANE Select	c.*11G>A		3_prime_UTR	Exon 16 of 16	NP_001229738.1	Q9Y2G4-2
	ANKRD6	NM_001242811.1		c.*11G>A		3_prime_UTR	Exon 16 of 16	NP_001229740.1	Q9Y2G4-2
	ANKRD6	NM_014942.4		c.*11G>A		3_prime_UTR	Exon 16 of 16	NP_055757.3	Q9Y2G4-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD6	ENST00000339746.9	TSL:1 MANE Select	c.*11G>A		3_prime_UTR	Exon 16 of 16	ENSP00000345767.4	Q9Y2G4-2
	ANKRD6	ENST00000447838.6	TSL:1	c.*11G>A		3_prime_UTR	Exon 16 of 16	ENSP00000396771.2	Q9Y2G4-3
	ANKRD6	ENST00000369408.9	TSL:1	c.*11G>A		3_prime_UTR	Exon 15 of 15	ENSP00000358416.5	Q9Y2G4-1

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

GnomAD2 exomes AF: 0.176 AC: 19092 AN: 108432 AF XY: 0.175

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 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

African (AFR) AF: 0.170 AC: 4946 AN: 29090

American (AMR) AF: 0.137 AC: 3226 AN: 23542

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 4568 AN: 21484

East Asian (EAS) AF: 0.194 AC: 6923 AN: 35738

South Asian (SAS) AF: 0.109 AC: 7533 AN: 69286

European-Finnish (FIN) AF: 0.173 AC: 7509 AN: 43476

Middle Eastern (MID) AF: 0.132 AC: 717 AN: 5412

European-Non Finnish (NFE) AF: 0.179 AC: 189309 AN: 1056440

Other (OTH) AF: 0.180 AC: 10020 AN: 55598

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

African (AFR) AF: 0.171 AC: 7083 AN: 41516

American (AMR) AF: 0.165 AC: 2524 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1131 AN: 5184

South Asian (SAS) AF: 0.113 AC: 544 AN: 4822

European-Finnish (FIN) AF: 0.182 AC: 1925 AN: 10580

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12060 AN: 67996

Other (OTH) AF: 0.182 AC: 382 AN: 2102

Alfa AF: 0.175 Hom.: 674

Bravo AF: 0.173

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.60
DANN	Benign	0.49
PhyloP100		-0.30
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: rs9344950; hg19: chr6-90340734;