rs8065577

Variant names:

• chr17-7481855-G-A
• rs8065577
• NM_001102614.2:c.4-133G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-7481855-G-A
• chr17-7481855-G-C
• chr17-7481855-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001102614.2(SLC35G6):​c.4-133G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000862 in 1,159,916 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 8.6e-7 (0 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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35G6	NM_001102614.2	c.4-133G>A		intron_variant	Intron 1 of 1	ENST00000412468.4	NP_001096084.1
ZBTB4	NM_020899.4	c.-81+2149C>T		intron_variant	Intron 1 of 3		NP_065950.2
SLC35G6	XM_047436533.1	c.10-133G>A		intron_variant	Intron 1 of 1		XP_047292489.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35G6	ENST00000412468.4	c.4-133G>A		intron_variant	Intron 1 of 1	1	NM_001102614.2	ENSP00000396523.2
ZBTB4	ENST00000311403.4	c.-81+2149C>T		intron_variant	Intron 1 of 3	1		ENSP00000307858.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 8.62e-7 AC: 1 AN: 1159916 Hom.: 0 AF XY: 0.00000176 AC XY: 1 AN XY: 568650

African (AFR) AF: 0.0000389 AC: 1 AN: 25688

American (AMR) AF: 0.00 AC: 0 AN: 19986

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18048

East Asian (EAS) AF: 0.00 AC: 0 AN: 34748

South Asian (SAS) AF: 0.00 AC: 0 AN: 60374

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40404

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4486

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 906974

Other (OTH) AF: 0.00 AC: 0 AN: 49208

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 2152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.77
PhyloP100		-1.5
PromoterAI		-0.0098	Neutral

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;