16-81041195-A-G

Variant names:

• chr16-81041195-A-G
• rs2970077
• ENST00000566488.1:c.-293A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000566488.1(ATMIN):​c.-293A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 706,352 control chromosomes in the GnomAD database, including 278,827 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 0.80 (51036 hom., cov: 32)
  • Exomes 𝑓: 0.90 (227791 hom.)
• Consequence: ATMIN ENST00000566488.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 13 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:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATMIN	NM_015251.3	c.337-161A>G		intron_variant	Intron 1 of 3	ENST00000299575.5	NP_056066.2
ATMIN	NM_001300728.2	c.-132-161A>G		intron_variant	Intron 1 of 3		NP_001287657.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATMIN	ENST00000299575.5	c.337-161A>G		intron_variant	Intron 1 of 3	1	NM_015251.3	ENSP00000299575.3
ENSG00000284512	ENST00000640345.1	c.425-6269T>C		intron_variant	Intron 4 of 5	5		ENSP00000492798.1

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121487 AN: 152068 Hom.: 51030 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.856

GnomAD4 exome AF: 0.904 AC: 500829 AN: 554166 Hom.: 227791 Cov.: 8 AF XY: 0.908 AC XY: 261417 AN XY: 287816

African (AFR) AF: 0.497 AC: 6851 AN: 13774

American (AMR) AF: 0.931 AC: 15164 AN: 16290

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 12456 AN: 13554

East Asian (EAS) AF: 0.926 AC: 27333 AN: 29530

South Asian (SAS) AF: 0.966 AC: 43543 AN: 45074

European-Finnish (FIN) AF: 0.859 AC: 34989 AN: 40754

Middle Eastern (MID) AF: 0.925 AC: 1945 AN: 2102

European-Non Finnish (NFE) AF: 0.914 AC: 333388 AN: 364858

Other (OTH) AF: 0.891 AC: 25160 AN: 28230

GnomAD4 genome AF: 0.798 AC: 121518 AN: 152186 Hom.: 51036 Cov.: 32 AF XY: 0.801 AC XY: 59598 AN XY: 74394

African (AFR) AF: 0.501 AC: 20772 AN: 41460

American (AMR) AF: 0.903 AC: 13805 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3186 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4823 AN: 5186

South Asian (SAS) AF: 0.965 AC: 4656 AN: 4826

European-Finnish (FIN) AF: 0.845 AC: 8957 AN: 10602

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62363 AN: 68028

Other (OTH) AF: 0.856 AC: 1807 AN: 2112

Alfa AF: 0.883 Hom.: 77871

Bravo AF: 0.788

Asia WGS AF: 0.923 AC: 3208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.68
PhyloP100		-0.38
Mutation Taster		=300/0	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: rs2970077; hg19: chr16-81074800;