NM_016108.4:c.141+2658C>G

Variant names:

• chr6-143063724-C-G
• rs10484584
• NM_016108.4:c.141+2658C>G

Variant summary

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

The NM_016108.4(AIG1):​c.141+2658C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 152,186 control chromosomes in the GnomAD database, including 239 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 0.027 (239 hom., cov: 33)
• Consequence: AIG1 NM_016108.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.805
• Publications: 1 publications found

Genes affected

AIG1 (HGNC:21607): (androgen induced 1) Enables hydrolase activity. Involved in long-chain fatty acid catabolic process. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AIG1	NM_016108.4	c.141+2658C>G		intron_variant	Intron 1 of 5	ENST00000357847.9	NP_057192.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AIG1	ENST00000357847.9	c.141+2658C>G		intron_variant	Intron 1 of 5	1	NM_016108.4	ENSP00000350509.4

Frequencies

GnomAD3 genomes AF: 0.0267 AC: 4067 AN: 152068 Hom.: 234 Cov.: 33

Gnomad AFR AF: 0.00959

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0152

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.0268

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0269 AC: 4088 AN: 152186 Hom.: 239 Cov.: 33 AF XY: 0.0293 AC XY: 2178 AN XY: 74404

African (AFR) AF: 0.00956 AC: 397 AN: 41536

American (AMR) AF: 0.155 AC: 2366 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3468

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5184

South Asian (SAS) AF: 0.0197 AC: 95 AN: 4826

European-Finnish (FIN) AF: 0.0152 AC: 161 AN: 10582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0113 AC: 767 AN: 67984

Other (OTH) AF: 0.0322 AC: 68 AN: 2114

Alfa AF: 0.0186 Hom.: 15

Bravo AF: 0.0378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.0
DANN	Benign	0.40
PhyloP100		0.81
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: rs10484584; hg19: chr6-143384861;