rs11081575

Variant names:

• chr18-79947525-G-A
• rs11081575
• NM_025078.5:c.203+3199C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-79947525-G-A
• chr18-79947525-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_025078.5(SLC66A2):​c.203+3199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00021 (0 hom., cov: 0)
• Consequence: SLC66A2 NM_025078.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 3 publications found

Genes affected

SLC66A2 (HGNC:26188): (solute carrier family 66 member 2) Predicted to be involved in phospholipid translocation and retrograde transport, endosome to Golgi. Predicted to be located in cytosol. Predicted to be integral component of membrane. Predicted to be active in endosome and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC66A2	NM_025078.5	c.203+3199C>T		intron_variant	Intron 2 of 5	ENST00000397778.7	NP_079354.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC66A2	ENST00000397778.7	c.203+3199C>T		intron_variant	Intron 2 of 5	1	NM_025078.5	ENSP00000380880.2

Frequencies

GnomAD3 genomes AF: 0.000207 AC: 7 AN: 33744 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00425

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000191

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000207 AC: 7 AN: 33744 Hom.: 0 Cov.: 0 AF XY: 0.000244 AC XY: 4 AN XY: 16406

African (AFR) AF: 0.00 AC: 0 AN: 16340

American (AMR) AF: 0.00 AC: 0 AN: 2048

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 512

East Asian (EAS) AF: 0.00425 AC: 5 AN: 1176

South Asian (SAS) AF: 0.00 AC: 0 AN: 1266

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1234

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 58

European-Non Finnish (NFE) AF: 0.000191 AC: 2 AN: 10478

Other (OTH) AF: 0.00 AC: 0 AN: 422

Alfa AF: 0.00 Hom.: 1221

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.90
PhyloP100		-0.013

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: rs11081575; hg19: chr18-77707525;