chr1-94870213-T-C

Variant names:

• chr1-94870213-T-C
• rs735937
• NM_001114106.3:c.1482+2796T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001114106.3(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 NM_001114106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001114106.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A3	NM_001114106.3	MANE Select	c.1482+2796T>C		intron	N/A	NP_001107578.1
	SLC44A3	NM_001258340.2		c.1479+2796T>C		intron	N/A	NP_001245269.1
	SLC44A3	NM_001258341.2		c.1383+2796T>C		intron	N/A	NP_001245270.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A3	ENST00000271227.11	TSL:1 MANE Select	c.1482+2796T>C		intron	N/A	ENSP00000271227.6
	SLC44A3	ENST00000467909.5	TSL:1	c.1338+2796T>C		intron	N/A	ENSP00000432789.1
	SLC44A3	ENST00000475883.5	TSL:1	n.*1205+2796T>C		intron	N/A	ENSP00000434457.1

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

African (AFR) AF: 0.241 AC: 10026 AN: 41522

American (AMR) AF: 0.350 AC: 5349 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1471 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2930 AN: 5178

South Asian (SAS) AF: 0.533 AC: 2572 AN: 4828

European-Finnish (FIN) AF: 0.496 AC: 5243 AN: 10564

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27578 AN: 67984

Other (OTH) AF: 0.379 AC: 801 AN: 2112

Alfa AF: 0.387 Hom.: 18940

Bravo AF: 0.353

Asia WGS AF: 0.516 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs735937; hg19: chr1-95335769;