rs859096

Variant names:

• chr1-94867512-G-A
• rs859096
• NM_001114106.3:c.1482+95G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-94867512-G-A
• chr1-94867512-G-C
• chr1-94867512-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001114106.3(SLC44A3):​c.1482+95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC44A3 NM_001114106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A3	NM_001114106.3	c.1482+95G>A		intron_variant	Intron 12 of 14	ENST00000271227.11	NP_001107578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A3	ENST00000271227.11	c.1482+95G>A		intron_variant	Intron 12 of 14	1	NM_001114106.3	ENSP00000271227.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 724586 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 368110

African (AFR) AF: 0.00 AC: 0 AN: 17116

American (AMR) AF: 0.00 AC: 0 AN: 23190

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14726

East Asian (EAS) AF: 0.00 AC: 0 AN: 31144

South Asian (SAS) AF: 0.00 AC: 0 AN: 39228

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44424

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3898

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 517452

Other (OTH) AF: 0.00 AC: 0 AN: 33408

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 25308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.26
PromoterAI		0.012	Neutral

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: rs859096; hg19: chr1-95333068;