chr4-687054-A-G

Variant names:

• chr4-687054-A-G
• rs7690350
• NM_032219.4:c.136-364T>C

Variant summary

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

The NM_032219.4(SLC49A3):​c.136-364T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,172 control chromosomes in the GnomAD database, including 5,475 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 0.25 (5475 hom., cov: 33)
• Consequence: SLC49A3 NM_032219.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 6 publications found

Genes affected

SLC49A3 (HGNC:26177): (solute carrier family 49 member 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC124900643 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC49A3	NM_032219.4	c.136-364T>C		intron_variant	Intron 1 of 9	ENST00000322224.9	NP_115595.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC49A3	ENST00000322224.9	c.136-364T>C		intron_variant	Intron 1 of 9	1	NM_032219.4	ENSP00000320234.4

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37837 AN: 152054 Hom.: 5446 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.249 AC: 37913 AN: 152172 Hom.: 5475 Cov.: 33 AF XY: 0.250 AC XY: 18572 AN XY: 74394

African (AFR) AF: 0.395 AC: 16403 AN: 41500

American (AMR) AF: 0.183 AC: 2798 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 696 AN: 3472

East Asian (EAS) AF: 0.257 AC: 1325 AN: 5162

South Asian (SAS) AF: 0.258 AC: 1244 AN: 4824

European-Finnish (FIN) AF: 0.221 AC: 2348 AN: 10602

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12403 AN: 68000

Other (OTH) AF: 0.231 AC: 489 AN: 2114

Alfa AF: 0.206 Hom.: 5186

Bravo AF: 0.252

Asia WGS AF: 0.266 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.33
PhyloP100		-2.1
PromoterAI		0.013	Neutral
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: rs7690350; hg19: chr4-680843;