rs7410943

Positions:

• chr1-197185891-A-G
• chr1-197185891-A-T

Variant summary

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

The NM_194314.3(ZBTB41):​c.1546+2401T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,962 control chromosomes in the GnomAD database, including 16,840 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 0.45 (16840 hom., cov: 31)
• Consequence: ZBTB41 NM_194314.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB41	NM_194314.3	c.1546+2401T>C		intron_variant		ENST00000367405.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB41	ENST00000367405.5	c.1546+2401T>C		intron_variant		1	NM_194314.3	P1
ZBTB41	ENST00000467322.1	c.1546+2401T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68294 AN: 151844 Hom.: 16825 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.450 AC: 68349 AN: 151962 Hom.: 16840 Cov.: 31 AF XY: 0.459 AC XY: 34123 AN XY: 74278

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.466

Alfa AF: 0.441 Hom.: 1927

Bravo AF: 0.449

Asia WGS AF: 0.705 AC: 2447 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.32

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: rs7410943; hg19: chr1-197155021;