17-7481855-G-C

Variant summary

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

The NM_001102614.2(SLC35G6):c.4-133G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 1,310,276 control chromosomes in the GnomAD database, including 370,528 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 0.73 (41268 hom., cov: 31)
  • Exomes 𝑓: 0.75 (329260 hom.)
• Consequence: SLC35G6 NM_001102614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

SLC35G6 (HGNC:31351): (solute carrier family 35 member G6) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB4 (HGNC:23847): (zinc finger and BTB domain containing 4) Enables several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; methyl-CpNpG binding activity; and sequence-specific DNA binding activity. Involved in cellular response to DNA damage stimulus and negative regulation of transcription by RNA polymerase II. Located in cytosol and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35G6	NM_001102614.2	c.4-133G>C		intron_variant		ENST00000412468.4
ZBTB4	NM_020899.4	c.-81+2149C>G		intron_variant
SLC35G6	XM_047436533.1	c.10-133G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35G6	ENST00000412468.4	c.4-133G>C		intron_variant		1	NM_001102614.2	P1
ZBTB4	ENST00000311403.4	c.-81+2149C>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111098 AN: 151934 Hom.: 41237 Cov.: 31

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.737

GnomAD4 exome AF: 0.753 AC: 871705 AN: 1158224 Hom.: 329260 AF XY: 0.752 AC XY: 427092 AN XY: 567814

Gnomad4 AFR exome AF: 0.611

Gnomad4 AMR exome AF: 0.836

Gnomad4 ASJ exome AF: 0.725

Gnomad4 EAS exome AF: 0.882

Gnomad4 SAS exome AF: 0.712

Gnomad4 FIN exome AF: 0.818

Gnomad4 NFE exome AF: 0.751

Gnomad4 OTH exome AF: 0.744

GnomAD4 genome AF: 0.731 AC: 111172 AN: 152052 Hom.: 41268 Cov.: 31 AF XY: 0.737 AC XY: 54783 AN XY: 74316

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.738

Alfa AF: 0.686 Hom.: 2152

Bravo AF: 0.724

Asia WGS AF: 0.813 AC: 2827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.9
Dann	Benign	0.58

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: rs8065577; hg19: chr17-7385174;