rs7531174

chr1-94872535-A-Gchr1-94872535-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001114106.3(SLC44A3):c.1482+5118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,108 control chromosomes in the GnomAD database, including 4,186 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 (4186 hom., cov: 32)
• Consequence: SLC44A3 NM_001114106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

SLC44A3 (HGNC:28689): (solute carrier family 44 member 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC44A3	NM_001114106.3	c.1482+5118A>G		intron_variant		ENST00000271227.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC44A3	ENST00000271227.11	c.1482+5118A>G		intron_variant		1	NM_001114106.3	P1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35117 AN: 151990 Hom.: 4181 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.231 AC: 35142 AN: 152108 Hom.: 4186 Cov.: 32 AF XY: 0.231 AC XY: 17179 AN XY: 74358

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.201

Alfa AF: 0.205 Hom.: 6525

Bravo AF: 0.236

Asia WGS AF: 0.240 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.016
Dann	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs7531174; hg19: chr1-95338091;