rs10423006

Variant names:

• chr19-47696087-C-G
• rs10423006
• NM_001394372.1:c.3187-364C>G

Your query was ambiguous. Multiple possible variants found:

• chr19-47696087-C-G
• chr19-47696087-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001394372.1(BICRA):​c.3187-364C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: BICRA NM_001394372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.28

Genes affected

BICRA (HGNC:4332): (BRD4 interacting chromatin remodeling complex associated protein) Enables transcription regulator activator activity. Involved in positive regulation of transcription, DNA-templated. Located in nucleus. Part of SWI/SNF complex. Implicated in Coffin-Siris syndrome. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000268746 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICRA	NM_001394372.1	c.3187-364C>G		intron_variant	Intron 10 of 14	ENST00000594866.3	NP_001381301.1
BICRA	NM_015711.3	c.3187-364C>G		intron_variant	Intron 10 of 14		NP_056526.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICRA	ENST00000594866.3	c.3187-364C>G		intron_variant	Intron 10 of 14	2	NM_001394372.1	ENSP00000469738.2
BICRA	ENST00000396720.7	c.3187-364C>G		intron_variant	Intron 10 of 14	5		ENSP00000379946.2
BICRA	ENST00000614245.2	c.2461-364C>G		intron_variant	Intron 5 of 9	5		ENSP00000480219.2
ENSG00000268746	ENST00000599924.1	n.87-35978C>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.091
DANN	Benign	0.45

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: rs10423006; hg19: chr19-48199344;