1-94824497-T-A

Variant names:

• chr1-94824497-T-A
• NM_001114106.3:c.140T>A

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001114106.3(SLC44A3):​c.140T>A​(p.Phe47Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC44A3 NM_001114106.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.68
• Publications: 0 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]

SLC44A3-AS1 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A3	NM_001114106.3	MANE Select	c.140T>A	p.Phe47Tyr	missense	Exon 3 of 15	NP_001107578.1	Q8N4M1-1
	SLC44A3	NM_001258340.2		c.140T>A	p.Phe47Tyr	missense	Exon 3 of 15	NP_001245269.1
	SLC44A3	NM_001258341.2		c.140T>A	p.Phe47Tyr	missense	Exon 3 of 15	NP_001245270.1	Q8N4M1-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A3	ENST00000271227.11	TSL:1 MANE Select	c.140T>A	p.Phe47Tyr	missense	Exon 3 of 15	ENSP00000271227.6	Q8N4M1-1
	SLC44A3	ENST00000467909.5	TSL:1	c.-5T>A		5_prime_UTR	Exon 2 of 14	ENSP00000432789.1	Q8N4M1-2
	SLC44A3	ENST00000475883.5	TSL:1	n.2T>A		non_coding_transcript_exon	Exon 1 of 14	ENSP00000434457.1	H0YDW5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Uncertain	0.066	T
BayesDel_noAF	Benign	-0.14
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.032	T
Eigen	Benign	0.091
Eigen_PC	Benign	0.066
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.64	T
M_CAP	Benign	0.048	D
MetaRNN	Uncertain	0.50	D
MetaSVM	Uncertain	-0.26	T
MutationAssessor	Uncertain	2.5	M
PhyloP100		4.7
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-1.3	N
REVEL	Benign	0.29
Sift	Benign	0.088	T
Sift4G	Benign	0.061	T
Polyphen		0.54	P
Vest4		0.65
MutPred		0.38		Gain of sheet (P = 0.1539)
MVP		0.87
MPC		0.67
ClinPred		0.96	D
GERP RS		4.6
Varity_R		0.23
gMVP		0.50
Mutation Taster		=65/35	polymorphism

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

hg19: chr1-95290053;