6-143296777-A-G

Variant names:

• chr6-143296777-A-G
• rs1885649
• NM_016108.4:c.515+12552A>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.515+12552A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,168 control chromosomes in the GnomAD database, including 42,195 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 0.73 (42195 hom., cov: 33)
• Consequence: AIG1 NM_016108.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• 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]

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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AIG1	NM_016108.4	c.515+12552A>G		intron_variant	Intron 4 of 5	ENST00000357847.9	NP_057192.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AIG1	ENST00000357847.9	c.515+12552A>G		intron_variant	Intron 4 of 5	1	NM_016108.4	ENSP00000350509.4

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110851 AN: 152050 Hom.: 42127 Cov.: 33

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.729 AC: 110982 AN: 152168 Hom.: 42195 Cov.: 33 AF XY: 0.735 AC XY: 54696 AN XY: 74370

African (AFR) AF: 0.927 AC: 38519 AN: 41548

American (AMR) AF: 0.736 AC: 11252 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1996 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5173 AN: 5180

South Asian (SAS) AF: 0.869 AC: 4193 AN: 4826

European-Finnish (FIN) AF: 0.607 AC: 6412 AN: 10566

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41286 AN: 67986

Other (OTH) AF: 0.685 AC: 1443 AN: 2106

Alfa AF: 0.657 Hom.: 12275

Bravo AF: 0.743

Asia WGS AF: 0.919 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.59
DANN	Benign	0.57
PhyloP100		-0.57
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: rs1885649; hg19: chr6-143617914;