19-14972983-C-G

Variant names:

• chr19-14972983-C-G
• rs8103212
• NM_005071.3:c.-7-66G>C

Variant summary

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

The NM_005071.3(SLC1A6):​c.-7-66G>C 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC1A6 NM_005071.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859
• Publications: 6 publications found

Genes affected

SLC1A6 (HGNC:10944): (solute carrier family 1 member 6) Predicted to enable high-affinity glutamate transmembrane transporter activity. Involved in neurotransmitter uptake. Located in intermediate filament cytoskeleton and 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=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005071.3. 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
	SLC1A6	NM_005071.3	MANE Select	c.-7-66G>C		intron	N/A	NP_005062.1	P48664-1
	SLC1A6	NM_001384669.1		c.-7-66G>C		intron	N/A	NP_001371598.1	P48664-1
	SLC1A6	NM_001272087.2		c.-7-66G>C		intron	N/A	NP_001259016.1	P48664-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A6	ENST00000594383.2	TSL:2 MANE Select	c.-7-66G>C		intron	N/A	ENSP00000472133.2	P48664-1
	SLC1A6	ENST00000600144.5	TSL:1	c.-7-66G>C		intron	N/A	ENSP00000471038.1	M0R063
	SLC1A6	ENST00000544886.6	TSL:1	c.-7-66G>C		intron	N/A	ENSP00000446175.1	P48664-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1133018 Hom.: 0 Cov.: 15 AF XY: 0.00 AC XY: 0 AN XY: 556692

African (AFR) AF: 0.00 AC: 0 AN: 25578

American (AMR) AF: 0.00 AC: 0 AN: 23210

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18950

East Asian (EAS) AF: 0.00 AC: 0 AN: 34042

South Asian (SAS) AF: 0.00 AC: 0 AN: 62424

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3374

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 872612

Other (OTH) AF: 0.00 AC: 0 AN: 48218

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 3024

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.84
DANN	Benign	0.68
PhyloP100		-0.86
PromoterAI		0.0056	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8103212; hg19: chr19-15083795;