rs1022092

Positions:

• chr6-111106083-G-A
• chr6-111106083-G-T

Variant summary

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

The NM_018593.5(SLC16A10):​c.343+17988G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,014 control chromosomes in the GnomAD database, including 16,460 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 0.44 (16460 hom., cov: 32)
• Consequence: SLC16A10 NM_018593.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549

Genes affected

SLC16A10 (HGNC:17027): (solute carrier family 16 member 10) SLC16A10 is a member of a family of plasma membrane amino acid transporters that mediate the Na(+)-independent transport of aromatic amino acids across the plasma membrane.[supplied by OMIM, Apr 2004]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A10	NM_018593.5	c.343+17988G>A		intron_variant		ENST00000368851.10
SLC16A10	XM_006715329.3	c.343+17988G>A		intron_variant
SLC16A10	XM_011535422.3	c.343+17988G>A		intron_variant
SLC16A10	XM_047418167.1	c.343+17988G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A10	ENST00000368851.10	c.343+17988G>A		intron_variant		1	NM_018593.5	P1

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66343 AN: 151894 Hom.: 16455 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.437 AC: 66356 AN: 152014 Hom.: 16460 Cov.: 32 AF XY: 0.437 AC XY: 32467 AN XY: 74308

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.472

Alfa AF: 0.522 Hom.: 26817

Bravo AF: 0.429

Asia WGS AF: 0.532 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.50

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: rs1022092; hg19: chr6-111427286;