1-94867512-G-T

Position:

• chr1-94867512-G-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+95G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 874,770 control chromosomes in the GnomAD database, including 214,520 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 0.62 (31236 hom., cov: 32)
  • Exomes 𝑓: 0.71 (183284 hom.)
• Consequence: SLC44A3 NM_001114106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

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]

SLC44A3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC44A3	NM_001114106.3	c.1482+95G>T		intron_variant		ENST00000271227.11	NP_001107578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC44A3	ENST00000271227.11	c.1482+95G>T		intron_variant		1	NM_001114106.3	ENSP00000271227.6

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94850 AN: 151936 Hom.: 31205 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.657

GnomAD4 exome AF: 0.708 AC: 511949 AN: 722714 Hom.: 183284 AF XY: 0.708 AC XY: 260115 AN XY: 367154

Gnomad4 AFR exome AF: 0.379

Gnomad4 AMR exome AF: 0.660

Gnomad4 ASJ exome AF: 0.704

Gnomad4 EAS exome AF: 0.804

Gnomad4 SAS exome AF: 0.687

Gnomad4 FIN exome AF: 0.765

Gnomad4 NFE exome AF: 0.714

Gnomad4 OTH exome AF: 0.693

GnomAD4 genome AF: 0.624 AC: 94926 AN: 152056 Hom.: 31236 Cov.: 32 AF XY: 0.629 AC XY: 46743 AN XY: 74320

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.661

Alfa AF: 0.675 Hom.: 20797

Bravo AF: 0.609

Asia WGS AF: 0.721 AC: 2505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.69

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: rs859096; hg19: chr1-95333068;