rs59358210

Variant names:

• chr14-23162163-G-A
• rs59358210
• NM_012244.4:c.508+3122C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012244.4. 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
	SLC7A8	NM_012244.4	MANE Select	c.508+3122C>T		intron	N/A	NP_036376.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC7A8	ENST00000316902.12	TSL:1 MANE Select	c.508+3122C>T		intron	N/A	ENSP00000320378.7
	SLC7A8	ENST00000469263.5	TSL:1	c.508+3122C>T		intron	N/A	ENSP00000435114.1

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

African (AFR) AF: 0.0233 AC: 966 AN: 41468

American (AMR) AF: 0.0913 AC: 1396 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 390 AN: 3464

East Asian (EAS) AF: 0.0651 AC: 337 AN: 5174

South Asian (SAS) AF: 0.202 AC: 968 AN: 4798

European-Finnish (FIN) AF: 0.112 AC: 1181 AN: 10564

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8126 AN: 67972

Other (OTH) AF: 0.0995 AC: 210 AN: 2110

Alfa AF: 0.0674 Hom.: 125

Bravo AF: 0.0844

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		2.4
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: rs59358210; hg19: chr14-23631372;