chrX-57120420-T-G

Variant names:

• chrX-57120420-T-G
• NM_001006681.2:c.210A>C

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001006681.2(SPIN2B):​c.210A>C​(p.Gly70Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 7)
  • Exomes 𝑓: 0.00015 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: SPIN2B NM_001006681.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0740
• Publications: 0 publications found

Genes affected

SPIN2B (HGNC:33147): (spindlin family member 2B) Enables methylated histone binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BP6: Variant X-57120420-T-G is Benign according to our data. Variant chrX-57120420-T-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2660712.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001006681.2. 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
	SPIN2B	NM_001006681.2	MANE Select	c.210A>C	p.Gly70Gly	synonymous	Exon 2 of 2	NP_001006682.1	Q9BPZ2
	SPIN2B	NM_001006682.2		c.210A>C	p.Gly70Gly	synonymous	Exon 2 of 2	NP_001006683.1	Q9BPZ2
	SPIN2B	NM_001006683.2		c.210A>C	p.Gly70Gly	synonymous	Exon 2 of 2	NP_001006684.1	Q9BPZ2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPIN2B	ENST00000434397.3	TSL:1 MANE Select	c.210A>C	p.Gly70Gly	synonymous	Exon 2 of 2	ENSP00000404314.2	Q9BPZ2
	SPIN2B	ENST00000275988.5	TSL:1	c.210A>C	p.Gly70Gly	synonymous	Exon 2 of 2	ENSP00000275988.5	Q9BPZ2
	SPIN2B	ENST00000333933.3	TSL:1	c.210A>C	p.Gly70Gly	synonymous	Exon 2 of 2	ENSP00000335008.3	Q9BPZ2

Frequencies

GnomAD3 genomes Cov.: 7

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000152 AC: 135 AN: 885531 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 226971

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000134 AC: 3 AN: 22403

American (AMR) AF: 0.00 AC: 0 AN: 33117

Ashkenazi Jewish (ASJ) AF: 0.0000590 AC: 1 AN: 16943

East Asian (EAS) AF: 0.00 AC: 0 AN: 29206

South Asian (SAS) AF: 0.00 AC: 0 AN: 45469

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38251

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3003

European-Non Finnish (NFE) AF: 0.000191 AC: 126 AN: 658100

Other (OTH) AF: 0.000128 AC: 5 AN: 39039

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 7

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	10
DANN	Benign	0.67
PhyloP100		-0.074
PromoterAI		-0.025	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

Other links and lift over

hg19: chrX-57146853;