chr10-93926824-C-G

Position:

• chr10-93926824-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000605679.5(SLC35G1):​c.*253+14025C>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,998 control chromosomes in the GnomAD database, including 18,481 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 0.48 (18481 hom., cov: 32)
• Consequence: SLC35G1 ENST00000605679.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.900

Genes affected

SLC35G1 (HGNC:26607): (solute carrier family 35 member G1) This gene encodes a transmembrane protein which is a member of the drug/metabolite transporter protein superfamily. The encoded protein may play a role in the regulation of calcium levels inside the cell. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35G1	ENST00000605679.5	c.*253+14025C>G		intron_variant, NMD_transcript_variant		1		ENSP00000474890
SLC35G1	ENST00000494992.5	c.*253+14025C>G		intron_variant, NMD_transcript_variant		5		ENSP00000474294

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73423 AN: 151880 Hom.: 18472 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.483 AC: 73474 AN: 151998 Hom.: 18481 Cov.: 32 AF XY: 0.490 AC XY: 36378 AN XY: 74288

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.449

Alfa AF: 0.460 Hom.: 1978

Bravo AF: 0.481

Asia WGS AF: 0.730 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs829237; hg19: chr10-95686581;