11-122979270-G-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Moderate BP6_Moderate BP7

The NM_001098169.2(BSX):c.450C>T(p.Ser150=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 1,611,462 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00082 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0012 (2 hom.)
• Consequence: BSX NM_001098169.2 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.10

Genes affected

BSX (HGNC:20450): (brain specific homeobox) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including eating behavior; mammary gland involution; and positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BP6: Variant 11-122979270-G-A is Benign according to our data. Variant chr11-122979270-G-A is described in ClinVar as [Benign]. Clinvar id is 727705.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.1 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BSX	NM_001098169.2	c.450C>T	p.Ser150=	synonymous_variant	2/3	ENST00000343035.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BSX	ENST00000343035.3	c.450C>T	p.Ser150=	synonymous_variant	2/3	5	NM_001098169.2	P1

Frequencies

GnomAD3 genomes AF: 0.000821 AC: 125 AN: 152176 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000655

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00123

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00138

Gnomad OTH AF: 0.000956

GnomAD3 exomes AF: 0.00142 AC: 351 AN: 247314 Hom.: 0 AF XY: 0.00133 AC XY: 178 AN XY: 134274

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000641

Gnomad ASJ exome AF: 0.000803

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000657

Gnomad FIN exome AF: 0.00322

Gnomad NFE exome AF: 0.00212

Gnomad OTH exome AF: 0.00217

GnomAD4 exome AF: 0.00117 AC: 1702 AN: 1459168 Hom.: 2 Cov.: 31 AF XY: 0.00114 AC XY: 826 AN XY: 725492

Gnomad4 AFR exome AF: 0.000150

Gnomad4 AMR exome AF: 0.000539

Gnomad4 ASJ exome AF: 0.000807

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000929

Gnomad4 FIN exome AF: 0.00332

Gnomad4 NFE exome AF: 0.00126

Gnomad4 OTH exome AF: 0.00113

GnomAD4 genome AF: 0.000821 AC: 125 AN: 152294 Hom.: 0 Cov.: 32 AF XY: 0.000739 AC XY: 55 AN XY: 74468

Gnomad4 AFR AF: 0.000120

Gnomad4 AMR AF: 0.000654

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00123

Gnomad4 NFE AF: 0.00138

Gnomad4 OTH AF: 0.000946

Alfa AF: 0.000978 Hom.: 0

Bravo AF: 0.000620

EpiCase AF: 0.000872

EpiControl AF: 0.00202

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jul 26, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	3.8
Dann	Benign	0.86

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: rs190227799; hg19: chr11-122849978;