1-94870213-T-C

Position:

• chr1-94870213-T-C

Variant summary

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

The ENST00000271227.11(SLC44A3):​c.1482+2796T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,146 control chromosomes in the GnomAD database, including 11,098 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 (11098 hom., cov: 33)
• Consequence: SLC44A3 ENST00000271227.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC44A3	NM_001114106.3	c.1482+2796T>C		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+2796T>C		intron_variant		1	NM_001114106.3	ENSP00000271227	P1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56333 AN: 152028 Hom.: 11102 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.370 AC: 56333 AN: 152146 Hom.: 11098 Cov.: 33 AF XY: 0.377 AC XY: 28025 AN XY: 74372

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.379

Alfa AF: 0.393 Hom.: 15236

Bravo AF: 0.353

Asia WGS AF: 0.516 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.6
DANN	Benign	0.66

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: rs735937; hg19: chr1-95335769;