rs4646768

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-126101728-T-A
• chr3-126101728-T-C
• chr3-126101728-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000507924.2(ALDH1L1-AS1):​n.628-1729T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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>A		intron	N/A
	SLC41A3	NM_001164475.2		c.-378A>T		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>A		intron	N/A
	SLC41A3	ENST00000910125.1		c.-327A>T		upstream_gene	N/A	ENSP00000580184.1
	SLC41A3	ENST00000508835.5	TSL:2	c.-378A>T		upstream_gene	N/A	ENSP00000427409.1	Q96GZ6-8

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-1.0
PromoterAI		-0.034	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;