rs17207629

Positions:

• chr6-31836833-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000375640.7(SNHG32):​n.635-403G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 273,672 control chromosomes in the GnomAD database, including 202 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 0.030 (106 hom., cov: 31)
  • Exomes 𝑓: 0.036 (96 hom.)
• Consequence: SNHG32 ENST00000375640.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

SNHG32 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.03 (4559/152162) while in subpopulation NFE AF= 0.046 (3127/67966). AF 95% confidence interval is 0.0447. There are 106 homozygotes in gnomad4. There are 2129 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 106 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNHG32	NR_160945.1	n.286-403G>A		intron_variant
SNHG32	NR_160946.1	n.431+316G>A		intron_variant
SNHG32	NR_160947.1	n.274+316G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNHG32	ENST00000375640.7	n.635-403G>A		intron_variant		1
SNHG32	ENST00000375633.5	n.165-403G>A		intron_variant		2
SNHG32	ENST00000375635.6	n.192-403G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0300 AC: 4555 AN: 152044 Hom.: 106 Cov.: 31

Gnomad AFR AF: 0.00669

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0189

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0297

GnomAD4 exome AF: 0.0362 AC: 4403 AN: 121510 Hom.: 96 Cov.: 0 AF XY: 0.0345 AC XY: 2281 AN XY: 66152

Gnomad4 AFR exome AF: 0.00522

Gnomad4 AMR exome AF: 0.0242

Gnomad4 ASJ exome AF: 0.0104

Gnomad4 EAS exome AF: 0.00593

Gnomad4 SAS exome AF: 0.0206

Gnomad4 FIN exome AF: 0.0494

Gnomad4 NFE exome AF: 0.0453

Gnomad4 OTH exome AF: 0.0414

GnomAD4 genome AF: 0.0300 AC: 4559 AN: 152162 Hom.: 106 Cov.: 31 AF XY: 0.0286 AC XY: 2129 AN XY: 74382

Gnomad4 AFR AF: 0.00676

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.0189

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0460

Gnomad4 OTH AF: 0.0294

Alfa AF: 0.0393 Hom.: 106

Bravo AF: 0.0273

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.84
DANN	Benign	0.76

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: rs17207629; hg19: chr6-31804610;