16-58663882-C-T

Variant names:

• chr16-58663882-C-T
• rs8061077
• ENST00000934505.1:c.*3503G>A

Variant summary

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

The ENST00000934505.1(SLC38A7):​c.*3503G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,002 control chromosomes in the GnomAD database, including 3,198 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 0.20 (3198 hom., cov: 33)
• Consequence: SLC38A7 ENST00000934505.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 6 publications found

Genes affected

SLC38A7 (HGNC:25582): (solute carrier family 38 member 7) Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport and sodium ion transport. Predicted to be located in axon and neuronal cell body. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000934505.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC38A7	ENST00000934505.1		c.*3503G>A		3_prime_UTR	Exon 12 of 12	ENSP00000604564.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31047 AN: 151884 Hom.: 3186 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.205 AC: 31095 AN: 152002 Hom.: 3198 Cov.: 33 AF XY: 0.203 AC XY: 15063 AN XY: 74282

African (AFR) AF: 0.213 AC: 8837 AN: 41454

American (AMR) AF: 0.135 AC: 2060 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3464

East Asian (EAS) AF: 0.274 AC: 1409 AN: 5146

South Asian (SAS) AF: 0.199 AC: 958 AN: 4822

European-Finnish (FIN) AF: 0.205 AC: 2168 AN: 10554

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14234 AN: 67958

Other (OTH) AF: 0.190 AC: 400 AN: 2110

Alfa AF: 0.206 Hom.: 14087

Bravo AF: 0.202

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.40
PhyloP100		-0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs8061077; hg19: chr16-58697786;