chr16-30874900-C-G

Variant names:

• chr16-30874900-C-G
• rs11642603
• ENST00000572628.5:c.525+13960G>C

Variant summary

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

The ENST00000572628.5(BCL7C):​c.525+13960G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 152,258 control chromosomes in the GnomAD database, including 472 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 0.068 (472 hom., cov: 31)
• Consequence: BCL7C ENST00000572628.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 5 publications found

Genes affected

BCL7C (HGNC:1006): (BAF chromatin remodeling complex subunit BCL7C) This gene is identified by the similarity of its product to the N-terminal region of BCL7A protein. The BCL7A protein is encoded by the gene known to be directly involved in a three-way gene translocation in a Burkitt lymphoma cell line. The function of this gene has not yet been determined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL7C	NM_001286526.2	c.528+13960G>C		intron_variant	Intron 5 of 5		NP_001273455.1
BCL7C	XM_047434896.1	c.621+5324G>C		intron_variant	Intron 6 of 6		XP_047290852.1
BCL7C	XM_011545980.4	c.528+13960G>C		intron_variant	Intron 5 of 5		XP_011544282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL7C	ENST00000572628.5	c.525+13960G>C		intron_variant	Intron 5 of 5	1		ENSP00000459007.1
BCL7C	ENST00000380317.8	c.528+13960G>C		intron_variant	Intron 5 of 5	1		ENSP00000369674.4
BCL7C	ENST00000574418.5	n.*71+13960G>C		intron_variant	Intron 4 of 4	5		ENSP00000461177.1

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 10369 AN: 152140 Hom.: 472 Cov.: 31

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0555

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0347

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0681 AC: 10364 AN: 152258 Hom.: 472 Cov.: 31 AF XY: 0.0654 AC XY: 4867 AN XY: 74452

African (AFR) AF: 0.0213 AC: 886 AN: 41562

American (AMR) AF: 0.0554 AC: 848 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5158

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4832

European-Finnish (FIN) AF: 0.0568 AC: 603 AN: 10622

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7457 AN: 68000

Other (OTH) AF: 0.0657 AC: 139 AN: 2116

Alfa AF: 0.0402 Hom.: 33

Bravo AF: 0.0664

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.42
PhyloP100		0.072
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11642603; hg19: chr16-30886221;