5-151279426-T-C

Variant names:

• chr5-151279426-T-C
• rs10061997
• NM_181774.4:c.1144+1588A>G

Variant summary

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

The NM_181774.4(SLC36A3):​c.1144+1588A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,152 control chromosomes in the GnomAD database, including 6,211 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 0.23 (6211 hom., cov: 33)
• Consequence: SLC36A3 NM_181774.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.820
• Publications: 1 publications found

Genes affected

SLC36A3 (HGNC:19659): (solute carrier family 36 member 3) Predicted to enable amino acid transmembrane transporter activity. Predicted to be involved in amino acid transport and proton transmembrane transport. Predicted to be integral component of 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181774.4. 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
	SLC36A3	NM_181774.4	MANE Select	c.1144+1588A>G		intron	N/A	NP_861439.3
	SLC36A3	NM_001145017.2		c.1267+1588A>G		intron	N/A	NP_001138489.1	Q495N2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC36A3	ENST00000335230.8	TSL:1 MANE Select	c.1144+1588A>G		intron	N/A	ENSP00000334750.3	Q495N2-1
	SLC36A3	ENST00000377713.3	TSL:1	c.1267+1588A>G		intron	N/A	ENSP00000366942.3	Q495N2-3
	SLC36A3	ENST00000423071.2	TSL:2	n.3044+1588A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34289 AN: 152032 Hom.: 6198 Cov.: 33

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0676

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.226 AC: 34339 AN: 152152 Hom.: 6211 Cov.: 33 AF XY: 0.223 AC XY: 16573 AN XY: 74394

African (AFR) AF: 0.501 AC: 20787 AN: 41476

American (AMR) AF: 0.130 AC: 1988 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3472

East Asian (EAS) AF: 0.310 AC: 1607 AN: 5184

South Asian (SAS) AF: 0.217 AC: 1047 AN: 4824

European-Finnish (FIN) AF: 0.0676 AC: 716 AN: 10592

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7237 AN: 68000

Other (OTH) AF: 0.189 AC: 399 AN: 2110

Alfa AF: 0.169 Hom.: 508

Bravo AF: 0.243

Asia WGS AF: 0.265 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.5
DANN	Benign	0.68
PhyloP100		0.82
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10061997;

hg19: chr5-150658987;