rs4305276

Variant names:

• chr2-240555596-C-A
• rs4305276
• NM_001282771.3:c.147-541G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-240555596-C-A
• chr2-240555596-C-G
• chr2-240555596-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001282771.3(ANKMY1):​c.147-541G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ANKMY1 NM_001282771.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 13 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKMY1	NM_001282771.3	c.147-541G>T		intron_variant	Intron 2 of 17	ENST00000401804.6	NP_001269700.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKMY1	ENST00000401804.6	c.147-541G>T		intron_variant	Intron 2 of 17	1	NM_001282771.3	ENSP00000385887.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4246 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2356

African (AFR) AF: 0.00 AC: 0 AN: 98

American (AMR) AF: 0.00 AC: 0 AN: 960

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 40

East Asian (EAS) AF: 0.00 AC: 0 AN: 144

South Asian (SAS) AF: 0.00 AC: 0 AN: 376

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2398

Other (OTH) AF: 0.00 AC: 0 AN: 176

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 1555

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.13
PhyloP100		-2.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs4305276; hg19: chr2-241495013;