10-70113825-G-A

Variant names:

• chr10-70113825-G-A
• rs7908957
• NM_032797.6:c.*353C>T

Variant summary

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

The NM_032797.6(AIFM2):​c.*353C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 202,254 control chromosomes in the GnomAD database, including 6,769 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 0.25 (5944 hom., cov: 32)
  • Exomes 𝑓: 0.16 (825 hom.)
• Consequence: AIFM2 NM_032797.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 5 publications found

Genes affected

AIFM2 (HGNC:21411): (apoptosis inducing factor mitochondria associated 2) This gene encodes a flavoprotein oxidoreductase that binds single stranded DNA and is thought to contribute to apoptosis in the presence of bacterial and viral DNA. The expression of this gene is also found to be induced by tumor suppressor protein p53 in colon cancer cells. [provided by RefSeq, Nov 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032797.6. 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
	AIFM2	NM_032797.6	MANE Select	c.*353C>T		3_prime_UTR	Exon 9 of 9	NP_116186.1	Q9BRQ8-1
	AIFM2	NM_001198696.2		c.*353C>T		3_prime_UTR	Exon 9 of 9	NP_001185625.1	Q9BRQ8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AIFM2	ENST00000307864.3	TSL:1 MANE Select	c.*353C>T		3_prime_UTR	Exon 9 of 9	ENSP00000312370.1	Q9BRQ8-1
	AIFM2	ENST00000373248.5	TSL:1	c.*33+320C>T		intron	N/A	ENSP00000362345.1	Q9BRQ8-1
	AIFM2	ENST00000959267.1		c.*353C>T		3_prime_UTR	Exon 9 of 9	ENSP00000629326.1

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37644 AN: 151818 Hom.: 5937 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.240

GnomAD4 exome AF: 0.157 AC: 7921 AN: 50318 Hom.: 825 Cov.: 0 AF XY: 0.163 AC XY: 4241 AN XY: 26016

African (AFR) AF: 0.419 AC: 394 AN: 940

American (AMR) AF: 0.228 AC: 379 AN: 1664

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 268 AN: 1414

East Asian (EAS) AF: 0.313 AC: 411 AN: 1312

South Asian (SAS) AF: 0.246 AC: 1428 AN: 5812

European-Finnish (FIN) AF: 0.141 AC: 359 AN: 2544

Middle Eastern (MID) AF: 0.227 AC: 50 AN: 220

European-Non Finnish (NFE) AF: 0.124 AC: 4123 AN: 33290

Other (OTH) AF: 0.163 AC: 509 AN: 3122

GnomAD4 genome AF: 0.248 AC: 37688 AN: 151936 Hom.: 5944 Cov.: 32 AF XY: 0.252 AC XY: 18714 AN XY: 74264

African (AFR) AF: 0.429 AC: 17771 AN: 41398

American (AMR) AF: 0.245 AC: 3743 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3466

East Asian (EAS) AF: 0.365 AC: 1877 AN: 5136

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4820

European-Finnish (FIN) AF: 0.171 AC: 1801 AN: 10552

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9535 AN: 67972

Other (OTH) AF: 0.240 AC: 505 AN: 2104

Alfa AF: 0.180 Hom.: 1481

Bravo AF: 0.261

Asia WGS AF: 0.333 AC: 1159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.39
PhyloP100		-0.95
Mutation Taster		=100/0	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: rs7908957; hg19: chr10-71873581;