rs59358210

Positions:

• chr14-23162163-G-A
• chr14-23162163-G-C

Variant summary

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

The NM_012244.4(SLC7A8):​c.508+3122C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0916 in 152,036 control chromosomes in the GnomAD database, including 791 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 0.092 (791 hom., cov: 31)
• Consequence: SLC7A8 NM_012244.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43

Genes affected

SLC7A8 (HGNC:11066): (solute carrier family 7 member 8) Enables several functions, including neutral amino acid transmembrane transporter activity; thyroid hormone transmembrane transporter activity; and toxin transmembrane transporter activity. Involved in L-alanine import across plasma membrane; L-leucine import across plasma membrane; and thyroid hormone transport. Located in plasma membrane. Part of basolateral plasma membrane and microvillus 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC7A8	NM_012244.4	c.508+3122C>T		intron_variant		ENST00000316902.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC7A8	ENST00000316902.12	c.508+3122C>T		intron_variant		1	NM_012244.4	P1
SLC7A8	ENST00000469263.5	c.508+3122C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0918 AC: 13940 AN: 151918 Hom.: 792 Cov.: 31

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0916 AC: 13927 AN: 152036 Hom.: 791 Cov.: 31 AF XY: 0.0939 AC XY: 6979 AN XY: 74308

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.0913

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0651

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0995

Alfa AF: 0.0895 Hom.: 113

Bravo AF: 0.0844

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.76

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: rs59358210; hg19: chr14-23631372;