3-126101728-T-C

Variant names:

• chr3-126101728-T-C
• rs4646768
• ENST00000507924.2:n.628-1729T>C

Variant summary

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

The ENST00000507924.2(ALDH1L1-AS1):​n.628-1729T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,990 control chromosomes in the GnomAD database, including 15,336 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 0.44 (15336 hom., cov: 32)
• Consequence: ALDH1L1-AS1 ENST00000507924.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996
• Publications: 6 publications found

Genes affected

ALDH1L1-AS1 (HGNC:40244): (ALDH1L1 antisense RNA 1)

SLC41A3 (HGNC:31046): (solute carrier family 41 member 3) Predicted to enable cation transmembrane transporter activity. Predicted to be involved in cation transmembrane transport. Located in plasma 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507924.2. 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
	ALDH1L1-AS1	NR_190231.1		n.740-1729T>C		intron	N/A
	SLC41A3	NM_001164475.2		c.-378A>G		upstream_gene	N/A	NP_001157947.1	Q96GZ6-8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH1L1-AS1	ENST00000507924.2	TSL:3	n.628-1729T>C		intron	N/A
	SLC41A3	ENST00000910125.1		c.-327A>G		upstream_gene	N/A	ENSP00000580184.1
	SLC41A3	ENST00000508835.5	TSL:2	c.-378A>G		upstream_gene	N/A	ENSP00000427409.1	Q96GZ6-8

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66723 AN: 151872 Hom.: 15304 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.440 AC: 66809 AN: 151990 Hom.: 15336 Cov.: 32 AF XY: 0.438 AC XY: 32570 AN XY: 74282

African (AFR) AF: 0.582 AC: 24121 AN: 41442

American (AMR) AF: 0.349 AC: 5330 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1737 AN: 5136

South Asian (SAS) AF: 0.346 AC: 1666 AN: 4816

European-Finnish (FIN) AF: 0.476 AC: 5027 AN: 10570

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26227 AN: 67962

Other (OTH) AF: 0.424 AC: 894 AN: 2108

Alfa AF: 0.313 Hom.: 869

Bravo AF: 0.438

Asia WGS AF: 0.370 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-1.0
PromoterAI		-0.020	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4646768; hg19: chr3-125820571;