chr16-81037092-A-T

Variant names:

• chr16-81037092-A-T
• rs2602431
• NM_015251.3:c.336+886A>T

Variant summary

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

The NM_015251.3(ATMIN):​c.336+886A>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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ATMIN NM_015251.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 19 publications found

Genes affected

ATMIN (HGNC:29034): (ATM interactor) Enables dynein complex binding activity. Involved in positive regulation of transcription, DNA-templated. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000284512 (HGNC:):

CENPN-AS1 (HGNC:55106): (CENPN antisense RNA 1)

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=-0.74).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015251.3. 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
	ATMIN	NM_015251.3	MANE Select	c.336+886A>T		intron	N/A	NP_056066.2
	ATMIN	NM_001300728.2		c.-516A>T		upstream_gene	N/A	NP_001287657.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATMIN	ENST00000299575.5	TSL:1 MANE Select	c.336+886A>T		intron	N/A	ENSP00000299575.3
	ENSG00000284512	ENST00000640345.1	TSL:5	c.425-2166T>A		intron	N/A	ENSP00000492798.1
	ATMIN	ENST00000946484.1		c.336+886A>T		intron	N/A	ENSP00000616543.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 627560 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 293470

African (AFR) AF: 0.00 AC: 0 AN: 11630

American (AMR) AF: 0.00 AC: 0 AN: 706

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3876

East Asian (EAS) AF: 0.00 AC: 0 AN: 2682

South Asian (SAS) AF: 0.00 AC: 0 AN: 12228

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 212

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1252

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 574348

Other (OTH) AF: 0.00 AC: 0 AN: 20626

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	12
DANN	Benign	0.92
PhyloP100		-0.048
PromoterAI		0.026	Neutral

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: rs2602431; hg19: chr16-81070697;