chr18-79947525-G-T

Variant names:

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

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>A 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 0.44 (1130 hom., cov: 0)
  • Failed GnomAD Quality Control
• 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=-1.03).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025078.5. 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
	SLC66A2	NM_025078.5	MANE Select	c.203+3199C>A		intron	N/A	NP_079354.2
	SLC66A2	NM_001146345.2		c.203+3199C>A		intron	N/A	NP_001139817.1
	SLC66A2	NM_001146343.2		c.203+3199C>A		intron	N/A	NP_001139815.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC66A2	ENST00000397778.7	TSL:1 MANE Select	c.203+3199C>A		intron	N/A	ENSP00000380880.2
	SLC66A2	ENST00000357575.8	TSL:5	c.203+3199C>A		intron	N/A	ENSP00000350188.3
	SLC66A2	ENST00000478144.5	TSL:3	c.144-184C>A		intron	N/A	ENSP00000466491.1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 14816 AN: 33616 Hom.: 1114 Cov.: 0

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.552

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.455

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.441 AC: 14864 AN: 33680 Hom.: 1130 Cov.: 0 AF XY: 0.446 AC XY: 7314 AN XY: 16404

African (AFR) AF: 0.403 AC: 6567 AN: 16312

American (AMR) AF: 0.454 AC: 923 AN: 2034

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 245 AN: 512

East Asian (EAS) AF: 0.525 AC: 615 AN: 1172

South Asian (SAS) AF: 0.527 AC: 662 AN: 1256

European-Finnish (FIN) AF: 0.463 AC: 570 AN: 1232

Middle Eastern (MID) AF: 0.554 AC: 31 AN: 56

European-Non Finnish (NFE) AF: 0.473 AC: 4945 AN: 10458

Other (OTH) AF: 0.466 AC: 205 AN: 440

Alfa AF: 0.101 Hom.: 1221

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		-0.013
RBP_binding_hub_radar		0.77
RBP_regulation_power_radar		1.9
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: rs11081575; hg19: chr18-77707525;