chr1-94862651-G-T

Variant names:

• chr1-94862651-G-T
• rs10493879
• NM_001114106.3:c.1239-2092G>T

Variant summary

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

The NM_001114106.3(SLC44A3):​c.1239-2092G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 152,154 control chromosomes in the GnomAD database, including 606 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 0.083 (606 hom., cov: 32)
• Consequence: SLC44A3 NM_001114106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38
• Publications: 7 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A3	NM_001114106.3	c.1239-2092G>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.1239-2092G>T		intron_variant	Intron 10 of 14	1	NM_001114106.3	ENSP00000271227.6

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12606 AN: 152036 Hom.: 606 Cov.: 32

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0753

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

GnomAD4 genome AF: 0.0829 AC: 12607 AN: 152154 Hom.: 606 Cov.: 32 AF XY: 0.0802 AC XY: 5969 AN XY: 74388

African (AFR) AF: 0.0510 AC: 2118 AN: 41524

American (AMR) AF: 0.0486 AC: 742 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3472

East Asian (EAS) AF: 0.0140 AC: 72 AN: 5160

South Asian (SAS) AF: 0.101 AC: 486 AN: 4816

European-Finnish (FIN) AF: 0.0719 AC: 762 AN: 10600

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7562 AN: 67988

Other (OTH) AF: 0.0741 AC: 156 AN: 2106

Alfa AF: 0.0943 Hom.: 414

Bravo AF: 0.0789

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0040
DANN	Benign	0.48
PhyloP100		-3.4
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: rs10493879; hg19: chr1-95328207;