rs4711279

Variant names:

• chr6-31834688-C-G
• rs4711279
• ENST00000375640.7:n.81C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-31834688-C-G
• chr6-31834688-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000375640.7(SNHG32):​n.81C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 318,178 control chromosomes in the GnomAD database, including 3,201 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 0.13 (1597 hom., cov: 30)
  • Exomes 𝑓: 0.13 (1604 hom.)
• Consequence: SNHG32 ENST00000375640.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649
• Publications: 21 publications found

Genes affected

SNHG32 (HGNC:19078): (small nucleolar RNA host gene 32) Predicted to enable double-stranded RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000375640.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG32	NR_160945.1		n.-228C>G		upstream_gene	N/A
	SNHG32	NR_160946.1		n.-228C>G		upstream_gene	N/A
	SNHG32	NR_160947.1		n.-228C>G		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG32	ENST00000375640.7	TSL:1	n.81C>G		non_coding_transcript_exon	Exon 1 of 4
	SNHG32	ENST00000375641.6	TSL:2	n.62C>G		non_coding_transcript_exon	Exon 1 of 4
	SNHG32	ENST00000718217.1		n.62C>G		non_coding_transcript_exon	Exon 1 of 5

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19154 AN: 151908 Hom.: 1597 Cov.: 30

Gnomad AFR AF: 0.0592

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.103

GnomAD4 exome AF: 0.128 AC: 21247 AN: 166152 Hom.: 1604 Cov.: 0 AF XY: 0.126 AC XY: 11525 AN XY: 91458

African (AFR) AF: 0.0562 AC: 221 AN: 3930

American (AMR) AF: 0.182 AC: 891 AN: 4906

Ashkenazi Jewish (ASJ) AF: 0.0388 AC: 148 AN: 3810

East Asian (EAS) AF: 0.139 AC: 743 AN: 5364

South Asian (SAS) AF: 0.125 AC: 4388 AN: 35146

European-Finnish (FIN) AF: 0.282 AC: 2261 AN: 8024

Middle Eastern (MID) AF: 0.0614 AC: 34 AN: 554

European-Non Finnish (NFE) AF: 0.119 AC: 11527 AN: 96518

Other (OTH) AF: 0.131 AC: 1034 AN: 7900

GnomAD4 genome AF: 0.126 AC: 19175 AN: 152026 Hom.: 1597 Cov.: 30 AF XY: 0.136 AC XY: 10121 AN XY: 74328

African (AFR) AF: 0.0593 AC: 2463 AN: 41524

American (AMR) AF: 0.187 AC: 2855 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3468

East Asian (EAS) AF: 0.147 AC: 759 AN: 5154

South Asian (SAS) AF: 0.138 AC: 667 AN: 4826

European-Finnish (FIN) AF: 0.328 AC: 3453 AN: 10542

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8474 AN: 67930

Other (OTH) AF: 0.103 AC: 217 AN: 2110

Alfa AF: 0.116 Hom.: 175

Bravo AF: 0.113

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.5
DANN	Benign	0.62
PhyloP100		0.65
Mutation Taster		=300/0	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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4711279;

hg19: chr6-31802465;