rs6499166

Variant names:

• chr16-68293014-G-A
• rs6499166
• NM_003983.6:c.1022+1353G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-68293014-G-A
• chr16-68293014-G-C

Variant summary

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

The NM_003983.6(SLC7A6):​c.1022+1353G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,184 control chromosomes in the GnomAD database, including 48,258 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 0.79 (48258 hom., cov: 32)
• Consequence: SLC7A6 NM_003983.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 9 publications found

Genes affected

SLC7A6 (HGNC:11064): (solute carrier family 7 member 6) Enables basic amino acid transmembrane transporter activity. Involved in basic amino acid transmembrane transport and ornithine transport. Located in intracellular membrane-bounded organelle and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC7A6OS (HGNC:25807): (solute carrier family 7 member 6 opposite strand) Predicted to be involved in developmental process. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be located in cytoplasm and nucleus. Implicated in progressive myoclonus epilepsy. [provided by Alliance of Genome Resources, Apr 2022]

SLC7A6OS Gene-Disease associations (from GenCC):

• epilepsy

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
• epilepsy, progressive myoclonic, 12

  Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000279649 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A6	NM_003983.6	c.1022+1353G>A		intron_variant	Intron 7 of 10	ENST00000219343.11	NP_003974.3
SLC7A6	NM_001076785.3	c.1022+1353G>A		intron_variant	Intron 8 of 11		NP_001070253.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A6	ENST00000219343.11	c.1022+1353G>A		intron_variant	Intron 7 of 10	1	NM_003983.6	ENSP00000219343.6

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120090 AN: 152066 Hom.: 48198 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.790 AC: 120213 AN: 152184 Hom.: 48258 Cov.: 32 AF XY: 0.787 AC XY: 58575 AN XY: 74402

African (AFR) AF: 0.944 AC: 39227 AN: 41548

American (AMR) AF: 0.779 AC: 11924 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2369 AN: 3470

East Asian (EAS) AF: 0.877 AC: 4545 AN: 5180

South Asian (SAS) AF: 0.692 AC: 3337 AN: 4822

European-Finnish (FIN) AF: 0.699 AC: 7391 AN: 10580

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 48977 AN: 67974

Other (OTH) AF: 0.760 AC: 1606 AN: 2112

Alfa AF: 0.730 Hom.: 20816

Bravo AF: 0.803

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		-0.034
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: rs6499166; hg19: chr16-68326917;