rs8056893

Positions:

• chr16-68270489-C-A
• chr16-68270489-C-G
• chr16-68270489-C-T

Variant summary

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

The ENST00000219343.11(SLC7A6):​c.-37+3768C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,130 control chromosomes in the GnomAD database, including 48,926 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 (48926 hom., cov: 32)
• Consequence: SLC7A6 ENST00000219343.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A6	NM_003983.6	c.-37+3768C>A		intron_variant		ENST00000219343.11	NP_003974.3
SLC7A6	NM_001076785.3	c.-123-3329C>A		intron_variant			NP_001070253.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A6	ENST00000219343.11	c.-37+3768C>A		intron_variant		1	NM_003983.6	ENSP00000219343	P1

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121116 AN: 152012 Hom.: 48867 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.797 AC: 121237 AN: 152130 Hom.: 48926 Cov.: 32 AF XY: 0.796 AC XY: 59164 AN XY: 74362

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.766

Alfa AF: 0.727 Hom.: 35187

Bravo AF: 0.806

Asia WGS AF: 0.779 AC: 2706 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	1.3
DANN	Benign	0.46

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

Publications

LitVar

Other links and lift over

dbSNP: rs8056893; hg19: chr16-68304392;