rs2285980

Variant names:

• chr19-14971600-G-A
• rs2285980
• NM_005071.3:c.343+137C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-14971600-G-A
• chr19-14971600-G-C
• chr19-14971600-G-T

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.343+137C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000224 in 847,624 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000026 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000022 (0 hom.)
• Consequence: SLC1A6 NM_005071.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 2 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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC1A6	NM_005071.3	c.343+137C>T		intron_variant	Intron 3 of 9	ENST00000594383.2	NP_005062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC1A6	ENST00000594383.2	c.343+137C>T		intron_variant	Intron 3 of 9	2	NM_005071.3	ENSP00000472133.2

Frequencies

GnomAD3 genomes AF: 0.0000263 AC: 4 AN: 151940 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000478

GnomAD4 exome AF: 0.0000216 AC: 15 AN: 695684 Hom.: 0 AF XY: 0.0000251 AC XY: 9 AN XY: 357854

African (AFR) AF: 0.00 AC: 0 AN: 17652

American (AMR) AF: 0.000128 AC: 3 AN: 23404

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15562

East Asian (EAS) AF: 0.00 AC: 0 AN: 33442

South Asian (SAS) AF: 0.00 AC: 0 AN: 53532

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35132

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2456

European-Non Finnish (NFE) AF: 0.0000208 AC: 10 AN: 480176

Other (OTH) AF: 0.0000583 AC: 2 AN: 34328

GnomAD4 genome AF: 0.0000263 AC: 4 AN: 151940 Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2 AN XY: 74196

African (AFR) AF: 0.00 AC: 0 AN: 41328

American (AMR) AF: 0.000197 AC: 3 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10578

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67982

Other (OTH) AF: 0.000478 AC: 1 AN: 2090

Alfa AF: 0.00 Hom.: 738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.93
PhyloP100		-0.10

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: rs2285980; hg19: chr19-15082412;