2-240555596-C-G

Variant summary

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

The NM_001282771.3(ANKMY1):c.147-541G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 155,640 control chromosomes in the GnomAD database, including 32,719 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 0.64 (31736 hom., cov: 33)
  • Exomes 𝑓: 0.67 (983 hom.)
• Consequence: ANKMY1 NM_001282771.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

Genes affected

ANKMY1 (HGNC:20987): (ankyrin repeat and MYND domain containing 1) Predicted to enable metal ion binding activity. [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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKMY1	NM_001282771.3	c.147-541G>C		intron_variant		ENST00000401804.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKMY1	ENST00000401804.6	c.147-541G>C		intron_variant		1	NM_001282771.3	P2

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97354 AN: 151288 Hom.: 31706 Cov.: 33

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.664

GnomAD4 exome AF: 0.667 AC: 2822 AN: 4234 Hom.: 983 Cov.: 0 AF XY: 0.679 AC XY: 1595 AN XY: 2348

Gnomad4 AFR exome AF: 0.459

Gnomad4 AMR exome AF: 0.592

Gnomad4 ASJ exome AF: 0.575

Gnomad4 EAS exome AF: 0.833

Gnomad4 SAS exome AF: 0.809

Gnomad4 FIN exome AF: 0.820

Gnomad4 NFE exome AF: 0.672

Gnomad4 OTH exome AF: 0.642

GnomAD4 genome AF: 0.644 AC: 97433 AN: 151406 Hom.: 31736 Cov.: 33 AF XY: 0.652 AC XY: 48237 AN XY: 74034

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.669

Alfa AF: 0.543 Hom.: 1555

Bravo AF: 0.631

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.29
Dann	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs4305276; hg19: chr2-241495013;