1-94859228-G-T

Variant names:

• chr1-94859228-G-T
• rs859101
• NM_001114106.3:c.1238+1728G>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.1238+1728G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,102 control chromosomes in the GnomAD database, including 11,531 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 (11531 hom., cov: 32)
• Consequence: SLC44A3 NM_001114106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 9 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC44A3	NM_001114106.3	MANE Select	c.1238+1728G>T		intron	N/A	NP_001107578.1	Q8N4M1-1
	SLC44A3	NM_001258340.2		c.1238+1728G>T		intron	N/A	NP_001245269.1
	SLC44A3	NM_001258341.2		c.1142+1728G>T		intron	N/A	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.1238+1728G>T		intron	N/A	ENSP00000271227.6	Q8N4M1-1
	SLC44A3	ENST00000467909.5	TSL:1	c.1094+1728G>T		intron	N/A	ENSP00000432789.1	Q8N4M1-2
	SLC44A3	ENST00000475883.5	TSL:1	n.*961+1728G>T		intron	N/A	ENSP00000434457.1	H0YDW5

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56098 AN: 151984 Hom.: 11533 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.369 AC: 56108 AN: 152102 Hom.: 11531 Cov.: 32 AF XY: 0.375 AC XY: 27859 AN XY: 74348

African (AFR) AF: 0.190 AC: 7897 AN: 41494

American (AMR) AF: 0.376 AC: 5745 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3472

East Asian (EAS) AF: 0.638 AC: 3298 AN: 5166

South Asian (SAS) AF: 0.556 AC: 2678 AN: 4820

European-Finnish (FIN) AF: 0.506 AC: 5343 AN: 10564

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28620 AN: 67970

Other (OTH) AF: 0.383 AC: 809 AN: 2114

Alfa AF: 0.398 Hom.: 20491

Bravo AF: 0.351

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.9
DANN	Benign	0.79
PhyloP100		-0.38
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: rs859101; hg19: chr1-95324784;