6-42756071-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001318819.2(BICRAL):c.-365+9048C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: BICRAL NM_001318819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

Genes affected

BICRAL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BICRAL	NM_001318819.2	c.-365+9048C>T		intron_variant
BICRAL	XM_047418542.1	c.-50-3770C>T		intron_variant
BICRAL	XM_047418543.1	c.-50-3770C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0966

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0939

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.169

Alfa AF: 0.167 Hom.: 3000

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

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: rs11759402; hg19: chr6-42723809;