rs3815501

Positions:

• chr2-200821399-T-C

Variant summary

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

The NM_001207067.2(BZW1):​c.1228+94T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 1,473,268 control chromosomes in the GnomAD database, including 471,296 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 0.78 (46618 hom., cov: 32)
  • Exomes 𝑓: 0.80 (424678 hom.)
• Consequence: BZW1 NM_001207067.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

Genes affected

BZW1 (HGNC:18380): (basic leucine zipper and W2 domains 1) Enables RNA binding activity and cadherin binding activity. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BZW1	NM_001207067.2	c.1228+94T>C		intron_variant		ENST00000409600.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BZW1	ENST00000409600.6	c.1228+94T>C		intron_variant		1	NM_001207067.2	P1
BZW1	ENST00000359893.4	c.375+94T>C		intron_variant		3
BZW1	ENST00000409226.5	c.1240+94T>C		intron_variant		2
BZW1	ENST00000452790.6	c.1324+94T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118309 AN: 152022 Hom.: 46593 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.779

GnomAD4 exome AF: 0.796 AC: 1052269 AN: 1321128 Hom.: 424678 AF XY: 0.792 AC XY: 518826 AN XY: 655294

Gnomad4 AFR exome AF: 0.773

Gnomad4 AMR exome AF: 0.596

Gnomad4 ASJ exome AF: 0.795

Gnomad4 EAS exome AF: 0.446

Gnomad4 SAS exome AF: 0.612

Gnomad4 FIN exome AF: 0.800

Gnomad4 NFE exome AF: 0.831

Gnomad4 OTH exome AF: 0.778

GnomAD4 genome AF: 0.778 AC: 118379 AN: 152140 Hom.: 46618 Cov.: 32 AF XY: 0.768 AC XY: 57143 AN XY: 74376

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.778

Alfa AF: 0.810 Hom.: 67931

Bravo AF: 0.773

Asia WGS AF: 0.546 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.56

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: rs3815501; hg19: chr2-201686122; COSMIC: COSV63350596; COSMIC: COSV63350596;