chr6-42867749-C-T

Variant names:

• chr6-42867749-C-T
• rs7764865
• NM_001393499.1:c.*2303C>T

Variant summary

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

The NM_001393499.1(BICRAL):​c.*2303C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,096 control chromosomes in the GnomAD database, including 5,362 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 0.20 (5362 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BICRAL NM_001393499.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 8 publications found

Genes affected

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393499.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICRAL	NM_001393499.1	MANE Select	c.*2303C>T		3_prime_UTR	Exon 13 of 13	NP_001380428.1
	BICRAL	NM_001318819.2		c.*2303C>T		3_prime_UTR	Exon 14 of 14	NP_001305748.1
	BICRAL	NM_015349.3		c.*2303C>T		3_prime_UTR	Exon 12 of 12	NP_056164.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICRAL	ENST00000314073.10	TSL:1 MANE Select	c.*2303C>T		3_prime_UTR	Exon 13 of 13	ENSP00000313933.4
	BICRAL	ENST00000394168.1	TSL:1	c.*2303C>T		3_prime_UTR	Exon 12 of 12	ENSP00000377723.1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30006 AN: 151978 Hom.: 5347 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0762

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.168

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.198 AC: 30074 AN: 152096 Hom.: 5362 Cov.: 32 AF XY: 0.196 AC XY: 14582 AN XY: 74364

African (AFR) AF: 0.481 AC: 19921 AN: 41430

American (AMR) AF: 0.137 AC: 2088 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3472

East Asian (EAS) AF: 0.116 AC: 599 AN: 5184

South Asian (SAS) AF: 0.185 AC: 895 AN: 4830

European-Finnish (FIN) AF: 0.0762 AC: 807 AN: 10594

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

European-Non Finnish (NFE) AF: 0.0709 AC: 4820 AN: 68000

Other (OTH) AF: 0.174 AC: 367 AN: 2114

Alfa AF: 0.120 Hom.: 3231

Bravo AF: 0.214

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.63
PhyloP100		0.30
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: rs7764865; hg19: chr6-42835487;