rs7690350

chr4-687054-A-Gchr4-687054-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC49A3	NM_032219.4	c.136-364T>C		intron_variant		ENST00000322224.9
LOC124900643	XR_007057985.1	n.370A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC49A3	ENST00000322224.9	c.136-364T>C		intron_variant		1	NM_032219.4	P4

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

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.231

Alfa AF: 0.204 Hom.: 3199

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7690350; hg19: chr4-680843;