rs8056893

Variant names:

• chr16-68270489-C-A
• rs8056893
• NM_003983.6:c.-37+3768C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_003983.6(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 NM_003983.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 30 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]

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 = 0.927 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003983.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC7A6	NM_003983.6	MANE Select	c.-37+3768C>A		intron	N/A	NP_003974.3	Q92536
	SLC7A6	NM_001076785.3		c.-123-3329C>A		intron	N/A	NP_001070253.1	Q92536

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC7A6	ENST00000219343.11	TSL:1 MANE Select	c.-37+3768C>A		intron	N/A	ENSP00000219343.6	Q92536
	SLC7A6	ENST00000379152.7	TSL:1	n.-37+3768C>A		intron	N/A	ENSP00000368448.3	E7EPZ8
	SLC7A6	ENST00000566454.5	TSL:5	c.-123-3329C>A		intron	N/A	ENSP00000455064.1	Q92536

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

African (AFR) AF: 0.935 AC: 38834 AN: 41548

American (AMR) AF: 0.777 AC: 11872 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2421 AN: 3470

East Asian (EAS) AF: 0.899 AC: 4657 AN: 5180

South Asian (SAS) AF: 0.721 AC: 3477 AN: 4822

European-Finnish (FIN) AF: 0.737 AC: 7783 AN: 10558

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49728 AN: 67958

Other (OTH) AF: 0.766 AC: 1619 AN: 2114

Alfa AF: 0.745 Hom.: 110180

Bravo AF: 0.806

Asia WGS AF: 0.779 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.16
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: rs8056893; hg19: chr16-68304392;