rs6499165

Positions:

• chr16-68292297-A-C
• chr16-68292297-A-G
• chr16-68292297-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003983.6(SLC7A6):​c.1022+636A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,182 control chromosomes in the GnomAD database, including 48,892 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 0.80 (48884 hom., cov: 31)
  • Exomes 𝑓: 0.61 (8 hom.)
• Consequence: SLC7A6 NM_003983.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

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]

(HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC7A6	NM_003983.6	c.1022+636A>C		intron_variant		ENST00000219343.11
SLC7A6	NM_001076785.3	c.1022+636A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC7A6	ENST00000219343.11	c.1022+636A>C		intron_variant		1	NM_003983.6	P1
	ENST00000623181.1	n.494T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120909 AN: 152020 Hom.: 48823 Cov.: 31

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.772

GnomAD4 exome AF: 0.614 AC: 27 AN: 44 Hom.: 8 Cov.: 0 AF XY: 0.688 AC XY: 22 AN XY: 32

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.550

Gnomad4 NFE exome AF: 0.714

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.796 AC: 121032 AN: 152138 Hom.: 48884 Cov.: 31 AF XY: 0.793 AC XY: 58943 AN XY: 74362

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.769

Alfa AF: 0.739 Hom.: 37085

Bravo AF: 0.809

Asia WGS AF: 0.772 AC: 2684 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	3.5
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6499165; hg19: chr16-68326200;