rs4711274

chr6-31615389-G-A

Variant summary

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

The NM_001623.5(AIF1):c.25+35G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,612,118 control chromosomes in the GnomAD database, including 17,003 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 0.14 (1830 hom., cov: 31)
  • Exomes 𝑓: 0.13 (15173 hom.)
• Consequence: AIF1 NM_001623.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

Genes affected

AIF1 (HGNC:352): (allograft inflammatory factor 1) This gene encodes a protein that binds actin and calcium. This gene is induced by cytokines and interferon and may promote macrophage activation and growth of vascular smooth muscle cells and T-lymphocytes. Polymorphisms in this gene may be associated with systemic sclerosis. Alternative splicing results in multiple transcript variants, but the full-length and coding nature of some of these variants is not certain. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AIF1	NM_001623.5	c.25+35G>A		intron_variant		ENST00000376059.8
AIF1	NM_001318970.2	c.-138+96G>A		intron_variant
AIF1	XM_005248870.5	c.25+35G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AIF1	ENST00000376059.8	c.25+35G>A		intron_variant		1	NM_001623.5	P1
AIF1	ENST00000337917.11	c.67+96G>A		intron_variant		1
AIF1	ENST00000466820.1	n.75+35G>A		intron_variant, non_coding_transcript_variant		5
AIF1	ENST00000497362.5	n.77+96G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21424 AN: 151958 Hom.: 1826 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0308

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.109

GnomAD3 exomes AF: 0.151 AC: 37856 AN: 251180 Hom.: 3594 AF XY: 0.143 AC XY: 19447 AN XY: 135786

Gnomad AFR exome AF: 0.106

Gnomad AMR exome AF: 0.233

Gnomad ASJ exome AF: 0.0297

Gnomad EAS exome AF: 0.140

Gnomad SAS exome AF: 0.0916

Gnomad FIN exome AF: 0.314

Gnomad NFE exome AF: 0.130

Gnomad OTH exome AF: 0.135

GnomAD4 exome AF: 0.134 AC: 195719 AN: 1460042 Hom.: 15173 Cov.: 38 AF XY: 0.131 AC XY: 95384 AN XY: 726414

Gnomad4 AFR exome AF: 0.0907

Gnomad4 AMR exome AF: 0.223

Gnomad4 ASJ exome AF: 0.0313

Gnomad4 EAS exome AF: 0.215

Gnomad4 SAS exome AF: 0.0905

Gnomad4 FIN exome AF: 0.311

Gnomad4 NFE exome AF: 0.127

Gnomad4 OTH exome AF: 0.121

GnomAD4 genome AF: 0.141 AC: 21451 AN: 152076 Hom.: 1830 Cov.: 31 AF XY: 0.149 AC XY: 11061 AN XY: 74344

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.0308

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0972

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.108

Alfa AF: 0.119 Hom.: 222

Bravo AF: 0.131

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.6
Dann	Benign	0.58

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: rs4711274; hg19: chr6-31583166; COSMIC: COSV61962464; COSMIC: COSV61962464;