chr1-94872535-A-G

Variant names:

• chr1-94872535-A-G
• rs7531174
• NM_001114106.3:c.1482+5118A>G

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+5118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,108 control chromosomes in the GnomAD database, including 4,186 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 0.23 (4186 hom., cov: 32)
• Consequence: SLC44A3 NM_001114106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 14 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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+5118A>G		intron	N/A	NP_001107578.1
	SLC44A3	NM_001258340.2		c.1479+5118A>G		intron	N/A	NP_001245269.1
	SLC44A3	NM_001258341.2		c.1383+5118A>G		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+5118A>G		intron	N/A	ENSP00000271227.6
	SLC44A3	ENST00000467909.5	TSL:1	c.1338+5118A>G		intron	N/A	ENSP00000432789.1
	SLC44A3	ENST00000475883.5	TSL:1	n.*1205+5118A>G		intron	N/A	ENSP00000434457.1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35117 AN: 151990 Hom.: 4181 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.231 AC: 35142 AN: 152108 Hom.: 4186 Cov.: 32 AF XY: 0.231 AC XY: 17179 AN XY: 74358

African (AFR) AF: 0.289 AC: 11999 AN: 41466

American (AMR) AF: 0.236 AC: 3609 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3472

East Asian (EAS) AF: 0.225 AC: 1161 AN: 5168

South Asian (SAS) AF: 0.272 AC: 1312 AN: 4830

European-Finnish (FIN) AF: 0.189 AC: 1999 AN: 10566

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13512 AN: 67994

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.209 Hom.: 14662

Bravo AF: 0.236

Asia WGS AF: 0.240 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.016
DANN	Benign	0.55
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs7531174; hg19: chr1-95338091;