chr6-31833091-G-C

Variant names:

• chr6-31833091-G-C
• rs2471980
• ENST00000649802.1:n.921-2320G>C

Variant summary

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

The ENST00000649802.1(SNHG32):​n.921-2320G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,794 control chromosomes in the GnomAD database, including 13,974 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 0.41 (13974 hom., cov: 31)
• Consequence: SNHG32 ENST00000649802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 22 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649802.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG32	ENST00000649802.1		n.921-2320G>C		intron	N/A
	SNHG32	ENST00000718216.1		n.365-2320G>C		intron	N/A
	SNHG32	ENST00000718219.1		n.185-2320G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62514 AN: 151676 Hom.: 13953 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.412 AC: 62585 AN: 151794 Hom.: 13974 Cov.: 31 AF XY: 0.414 AC XY: 30699 AN XY: 74172

African (AFR) AF: 0.584 AC: 24151 AN: 41370

American (AMR) AF: 0.408 AC: 6225 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3466

East Asian (EAS) AF: 0.267 AC: 1376 AN: 5150

South Asian (SAS) AF: 0.372 AC: 1790 AN: 4814

European-Finnish (FIN) AF: 0.452 AC: 4745 AN: 10506

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22145 AN: 67936

Other (OTH) AF: 0.410 AC: 864 AN: 2106

Alfa AF: 0.309 Hom.: 4074

Bravo AF: 0.417

Asia WGS AF: 0.432 AC: 1498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.59
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2471980; hg19: chr6-31800868;