chr11-122980855-C-A

Variant names:

• chr11-122980855-C-A
• rs1870761
• NM_001098169.2:c.262+555G>T

Variant summary

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

The NM_001098169.2(BSX):​c.262+555G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,906 control chromosomes in the GnomAD database, including 11,972 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 0.39 (11972 hom., cov: 31)
• Consequence: BSX NM_001098169.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 4 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BSX	NM_001098169.2	c.262+555G>T		intron_variant	Intron 1 of 2	ENST00000343035.3	NP_001091639.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BSX	ENST00000343035.3	c.262+555G>T		intron_variant	Intron 1 of 2	5	NM_001098169.2	ENSP00000344285.2

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59811 AN: 151788 Hom.: 11965 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.394 AC: 59833 AN: 151906 Hom.: 11972 Cov.: 31 AF XY: 0.388 AC XY: 28796 AN XY: 74222

African (AFR) AF: 0.385 AC: 15925 AN: 41406

American (AMR) AF: 0.303 AC: 4627 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1463 AN: 3466

East Asian (EAS) AF: 0.285 AC: 1474 AN: 5164

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4812

European-Finnish (FIN) AF: 0.420 AC: 4434 AN: 10554

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29163 AN: 67928

Other (OTH) AF: 0.401 AC: 846 AN: 2110

Alfa AF: 0.414 Hom.: 22331

Bravo AF: 0.387

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.89
DANN	Benign	0.34
PhyloP100		0.026
Mutation Taster		=100/0	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

Other links and lift over

dbSNP: rs1870761; hg19: chr11-122851563;