6-42756071-C-T

Variant names:

• chr6-42756071-C-T
• rs11759402

Variant summary

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

The variant allele was found at a frequency of 0.148 in 152,170 control chromosomes in the GnomAD database, including 1,814 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 0.15 (1814 hom., cov: 31)
• Consequence: LOC124901226 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 9 publications found

Genes affected

LOC124901226 (HGNC:):

BICRAL (HGNC:21111): (BICRA like chromatin remodeling complex associated protein) Predicted to be involved in positive regulation of transcription, DNA-templated. Part of SWI/SNF complex. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901226		n.42756071C>T		intragenic_variant
BICRAL	NM_001318819.2	c.-365+9048C>T		intron_variant	Intron 1 of 13		NP_001305748.1
BICRAL	XM_047418542.1	c.-50-3770C>T		intron_variant	Intron 2 of 14		XP_047274498.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22525 AN: 152052 Hom.: 1805 Cov.: 31

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0939

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.148 AC: 22543 AN: 152170 Hom.: 1814 Cov.: 31 AF XY: 0.147 AC XY: 10952 AN XY: 74378

African (AFR) AF: 0.0966 AC: 4011 AN: 41542

American (AMR) AF: 0.151 AC: 2305 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3470

East Asian (EAS) AF: 0.0939 AC: 485 AN: 5166

South Asian (SAS) AF: 0.219 AC: 1057 AN: 4820

European-Finnish (FIN) AF: 0.143 AC: 1515 AN: 10582

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12253 AN: 67996

Other (OTH) AF: 0.169 AC: 357 AN: 2110

Alfa AF: 0.166 Hom.: 6571

Bravo AF: 0.145

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.041

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: rs11759402; hg19: chr6-42723809;