chr5-151492234-C-T

Variant names:

• chr5-151492234-C-T
• rs1175
• NM_078483.4:c.*3980C>T

Variant summary

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

The NM_078483.4(SLC36A1):​c.*3980C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,168 control chromosomes in the GnomAD database, including 2,331 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 0.17 (2330 hom., cov: 32)
  • Exomes 𝑓: 0.22 (1 hom.)
• Consequence: SLC36A1 NM_078483.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922
• Publications: 11 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC36A1	NM_078483.4	c.*3980C>T		3_prime_UTR_variant	Exon 11 of 11	ENST00000243389.8	NP_510968.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC36A1	ENST00000243389.8	c.*3980C>T		3_prime_UTR_variant	Exon 11 of 11	1	NM_078483.4	ENSP00000243389.3

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25949 AN: 152032 Hom.: 2330 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.180

GnomAD4 exome AF: 0.222 AC: 4 AN: 18 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 4 AN XY: 16

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 4 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.171 AC: 25954 AN: 152150 Hom.: 2330 Cov.: 32 AF XY: 0.167 AC XY: 12454 AN XY: 74396

African (AFR) AF: 0.145 AC: 6026 AN: 41492

American (AMR) AF: 0.148 AC: 2262 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 484 AN: 3468

East Asian (EAS) AF: 0.0254 AC: 132 AN: 5192

South Asian (SAS) AF: 0.0899 AC: 433 AN: 4816

European-Finnish (FIN) AF: 0.192 AC: 2036 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14087 AN: 67994

Other (OTH) AF: 0.179 AC: 377 AN: 2112

Alfa AF: 0.193 Hom.: 3640

Bravo AF: 0.165

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.070
DANN	Benign	0.61
PhyloP100		-0.92
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1175; hg19: chr5-150871795;