chr18-79947525-G-T

Position:

• chr18-79947525-G-T

Variant summary

Our verdict is Likely benign. Variant got -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

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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC66A2	NM_025078.5	c.203+3199C>A		intron_variant		ENST00000397778.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC66A2	ENST00000397778.7	c.203+3199C>A		intron_variant		1	NM_025078.5	P3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 14816 AN: 33616 Hom.: 1114 Cov.: 0 FAILED QC

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

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.466

Alfa AF: 0.0980 Hom.: 967

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.47
RBP_binding_hub_radar		0.77
RBP_regulation_power_radar		1.9

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

Publications

LitVar

Other links and lift over

dbSNP: rs11081575; hg19: chr18-77707525;