rs4350226

chr1-197163248-G-Achr1-197163248-G-Cchr1-197163248-G-T

Variant summary

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

The NM_194314.3(ZBTB41):c.2075-3234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,084 control chromosomes in the GnomAD database, including 51,749 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 0.81 (51749 hom., cov: 31)
• Consequence: ZBTB41 NM_194314.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

Genes affected

ZBTB41 (HGNC:24819): (zinc finger and BTB domain containing 41) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB41	NM_194314.3	c.2075-3234C>T		intron_variant		ENST00000367405.5
ZBTB41	XM_047419671.1	c.2075-3234C>T		intron_variant
ZBTB41	NR_135153.2	n.2347-3234C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB41	ENST00000367405.5	c.2075-3234C>T		intron_variant		1	NM_194314.3	P1
ZBTB41	ENST00000467322.1	c.*275-3234C>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.809 AC: 123001 AN: 151966 Hom.: 51708 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.809 AC: 123096 AN: 152084 Hom.: 51749 Cov.: 31 AF XY: 0.812 AC XY: 60355 AN XY: 74360

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.904

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.830

Alfa AF: 0.850 Hom.: 6986

Bravo AF: 0.797

Asia WGS AF: 0.929 AC: 3231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.9
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: rs4350226; hg19: chr1-197132378;