rs6908441

Positions:

• chr6-143159606-G-T

Variant summary

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

The ENST00000357847.9(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 ENST00000357847.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AIG1	NM_016108.4	c.298-5476G>T		intron_variant		ENST00000357847.9	NP_057192.2
LOC124901416	XR_007059794.1	n.185+5298C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AIG1	ENST00000357847.9	c.298-5476G>T		intron_variant		1	NM_016108.4	ENSP00000350509	P1

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

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.334

Alfa AF: 0.324 Hom.: 16735

Bravo AF: 0.335

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.9
DANN	Benign	0.77

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: rs6908441; hg19: chr6-143480743; COSMIC: COSV51632905;