chr5-151366473-A-G

Variant names:

• chr5-151366473-A-G
• rs10463316
• XM_011537591.2:c.-90+21739A>G

Variant summary

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

The ENST00000647906.1(ENSG00000290991):​n.1242T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 285,402 control chromosomes in the GnomAD database, including 21,636 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 0.37 (10548 hom., cov: 32)
  • Exomes 𝑓: 0.39 (11088 hom.)
• Consequence: ENSG00000290991 ENST00000647906.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 7 publications found

Genes affected

SLC36A1 (HGNC:18761): (solute carrier family 36 member 1) This gene encodes a member of the eukaryote-specific amino acid/auxin permease (AAAP) 1 transporter family. The encoded protein functions as a proton-dependent, small amino acid transporter. This gene is clustered with related family members on chromosome 5q33.1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

ENSG00000253897 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647906.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253897	ENST00000517788.1	TSL:6	n.1136T>C		non_coding_transcript_exon	Exon 9 of 9
	ENSG00000290991	ENST00000647906.1		n.1242T>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000297368	ENST00000747508.1		n.675+21739A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56193 AN: 151936 Hom.: 10544 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.354

GnomAD4 exome AF: 0.394 AC: 52525 AN: 133348 Hom.: 11088 Cov.: 0 AF XY: 0.400 AC XY: 31392 AN XY: 78564

African (AFR) AF: 0.339 AC: 818 AN: 2416

American (AMR) AF: 0.208 AC: 1393 AN: 6700

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1114 AN: 3060

East Asian (EAS) AF: 0.439 AC: 1100 AN: 2506

South Asian (SAS) AF: 0.428 AC: 9265 AN: 21628

European-Finnish (FIN) AF: 0.451 AC: 7780 AN: 17232

Middle Eastern (MID) AF: 0.249 AC: 178 AN: 714

European-Non Finnish (NFE) AF: 0.392 AC: 28652 AN: 73038

Other (OTH) AF: 0.368 AC: 2225 AN: 6054

GnomAD4 genome AF: 0.370 AC: 56235 AN: 152054 Hom.: 10548 Cov.: 32 AF XY: 0.371 AC XY: 27552 AN XY: 74312

African (AFR) AF: 0.349 AC: 14460 AN: 41462

American (AMR) AF: 0.269 AC: 4115 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2199 AN: 5154

South Asian (SAS) AF: 0.434 AC: 2089 AN: 4818

European-Finnish (FIN) AF: 0.452 AC: 4779 AN: 10568

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26103 AN: 67978

Other (OTH) AF: 0.356 AC: 750 AN: 2108

Alfa AF: 0.367 Hom.: 4634

Bravo AF: 0.352

Asia WGS AF: 0.421 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.2
DANN	Benign	0.51
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10463316; hg19: chr5-150746034;