rs6908441

Variant names:

• chr6-143159606-G-T
• rs6908441
• NM_016108.4:c.298-5476G>T

Variant summary

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

The NM_016108.4(AIG1):​c.298-5476G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,018 control chromosomes in the GnomAD database, including 8,055 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 0.32 (8055 hom., cov: 32)
• Consequence: AIG1 NM_016108.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 3 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]

LOC124901416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016108.4. 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
	AIG1	NM_016108.4	MANE Select	c.298-5476G>T		intron	N/A	NP_057192.2
	AIG1	NM_001366344.1		c.439-5476G>T		intron	N/A	NP_001353273.1
	AIG1	NM_001366345.1		c.370-5476G>T		intron	N/A	NP_001353274.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AIG1	ENST00000357847.9	TSL:1 MANE Select	c.298-5476G>T		intron	N/A	ENSP00000350509.4	Q9NVV5-2
	AIG1	ENST00000494282.6	TSL:1	c.298-5476G>T		intron	N/A	ENSP00000473952.1	Q9NVV5-5
	AIG1	ENST00000275235.8	TSL:2	c.298-5476G>T		intron	N/A	ENSP00000275235.4	Q9NVV5-1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49044 AN: 151900 Hom.: 8048 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.323 AC: 49072 AN: 152018 Hom.: 8055 Cov.: 32 AF XY: 0.319 AC XY: 23719 AN XY: 74310

African (AFR) AF: 0.342 AC: 14175 AN: 41454

American (AMR) AF: 0.379 AC: 5783 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3466

East Asian (EAS) AF: 0.154 AC: 796 AN: 5176

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4822

European-Finnish (FIN) AF: 0.237 AC: 2503 AN: 10554

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22013 AN: 67962

Other (OTH) AF: 0.334 AC: 707 AN: 2114

Alfa AF: 0.323 Hom.: 35402

Bravo AF: 0.335

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.9
DANN	Benign	0.77
PhyloP100		1.4
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: rs6908441; hg19: chr6-143480743; COSMIC: COSV51632905;