chr1-94859228-G-T

Variant names:

• chr1-94859228-G-T
• rs859101
• NM_001114106.3:c.1238+1728G>T

Variant summary

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

The NM_001114106.3(SLC44A3):​c.1238+1728G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,102 control chromosomes in the GnomAD database, including 11,531 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 0.37 (11531 hom., cov: 32)
• Consequence: SLC44A3 NM_001114106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A3	NM_001114106.3	c.1238+1728G>T		intron_variant	Intron 10 of 14	ENST00000271227.11	NP_001107578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A3	ENST00000271227.11	c.1238+1728G>T		intron_variant	Intron 10 of 14	1	NM_001114106.3	ENSP00000271227.6

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56098 AN: 151984 Hom.: 11533 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.369 AC: 56108 AN: 152102 Hom.: 11531 Cov.: 32 AF XY: 0.375 AC XY: 27859 AN XY: 74348

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.383

Alfa AF: 0.405 Hom.: 16577

Bravo AF: 0.351

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.9
DANN	Benign	0.79

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: rs859101; hg19: chr1-95324784;