rs2097837

Variant names:

• chr19-14968175-G-A
• rs2097837
• NM_005071.3:c.548+128C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-14968175-G-A
• chr19-14968175-G-C
• chr19-14968175-G-T

Variant summary

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

The NM_005071.3(SLC1A6):​c.548+128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 743,050 control chromosomes in the GnomAD database, including 40,781 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 0.34 (8695 hom., cov: 31)
  • Exomes 𝑓: 0.32 (32086 hom.)
• Consequence: SLC1A6 NM_005071.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC1A6	NM_005071.3	c.548+128C>T		intron_variant	Intron 4 of 9	ENST00000594383.2	NP_005062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC1A6	ENST00000594383.2	c.548+128C>T		intron_variant	Intron 4 of 9	2	NM_005071.3	ENSP00000472133.2

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50857 AN: 151626 Hom.: 8684 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.322

GnomAD4 exome AF: 0.322 AC: 190497 AN: 591308 Hom.: 32086 AF XY: 0.323 AC XY: 98371 AN XY: 304324

African (AFR) AF: 0.381 AC: 5823 AN: 15282

American (AMR) AF: 0.296 AC: 6784 AN: 22940

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 4526 AN: 15176

East Asian (EAS) AF: 0.0943 AC: 2979 AN: 31576

South Asian (SAS) AF: 0.341 AC: 16950 AN: 49640

European-Finnish (FIN) AF: 0.312 AC: 10397 AN: 33330

Middle Eastern (MID) AF: 0.359 AC: 851 AN: 2368

European-Non Finnish (NFE) AF: 0.339 AC: 132280 AN: 390198

Other (OTH) AF: 0.322 AC: 9907 AN: 30798

GnomAD4 genome AF: 0.335 AC: 50906 AN: 151742 Hom.: 8695 Cov.: 31 AF XY: 0.332 AC XY: 24595 AN XY: 74146

African (AFR) AF: 0.375 AC: 15506 AN: 41344

American (AMR) AF: 0.306 AC: 4664 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 997 AN: 3466

East Asian (EAS) AF: 0.111 AC: 572 AN: 5168

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4812

European-Finnish (FIN) AF: 0.315 AC: 3308 AN: 10516

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23160 AN: 67858

Other (OTH) AF: 0.320 AC: 675 AN: 2112

Alfa AF: 0.332 Hom.: 3494

Bravo AF: 0.333

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.45
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs2097837; hg19: chr19-15078987;