16-81037092-A-G

Variant names:

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

Variant summary

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

The NM_015251.3(ATMIN):​c.336+886A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 778,564 control chromosomes in the GnomAD database, including 280,940 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 0.74 (44581 hom., cov: 31)
  • Exomes 𝑓: 0.87 (236359 hom.)
• Consequence: ATMIN NM_015251.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATMIN	NM_015251.3	c.336+886A>G		intron_variant	Intron 1 of 3	ENST00000299575.5	NP_056066.2
CENPN-AS1	XR_007065134.1	n.3220T>C		non_coding_transcript_exon_variant	Exon 1 of 4
CENPN-AS1	XR_007065133.1	n.86+1375T>C		intron_variant	Intron 1 of 3
ATMIN	NM_001300728.2	c.-516A>G		upstream_gene_variant			NP_001287657.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATMIN	ENST00000299575.5	c.336+886A>G		intron_variant	Intron 1 of 3	1	NM_015251.3	ENSP00000299575.3
ENSG00000284512	ENST00000640345.1	c.425-2166T>C		intron_variant	Intron 4 of 5	5		ENSP00000492798.1

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113151 AN: 151938 Hom.: 44574 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.796

GnomAD4 exome AF: 0.866 AC: 542449 AN: 626508 Hom.: 236359 AF XY: 0.867 AC XY: 253951 AN XY: 292944

Gnomad4 AFR exome AF: 0.415

Gnomad4 AMR exome AF: 0.858

Gnomad4 ASJ exome AF: 0.906

Gnomad4 EAS exome AF: 0.729

Gnomad4 SAS exome AF: 0.880

Gnomad4 FIN exome AF: 0.821

Gnomad4 NFE exome AF: 0.876

Gnomad4 OTH exome AF: 0.847

GnomAD4 genome AF: 0.744 AC: 113183 AN: 152056 Hom.: 44581 Cov.: 31 AF XY: 0.744 AC XY: 55330 AN XY: 74342

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.795

Alfa AF: 0.862 Hom.: 91097

Bravo AF: 0.729

Asia WGS AF: 0.789 AC: 2743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.88

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: rs2602431; hg19: chr16-81070697;