chr1-197163248-G-A

Variant names:

• chr1-197163248-G-A
• rs4350226
• NM_194314.3:c.2075-3234C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_194314.3. 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
	ZBTB41	NM_194314.3	MANE Select	c.2075-3234C>T		intron	N/A	NP_919290.2
	ZBTB41	NR_135153.2		n.2347-3234C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB41	ENST00000367405.5	TSL:1 MANE Select	c.2075-3234C>T		intron	N/A	ENSP00000356375.3
	ZBTB41	ENST00000467322.1	TSL:2	n.*275-3234C>T		intron	N/A	ENSP00000502173.1

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

African (AFR) AF: 0.552 AC: 22875 AN: 41444

American (AMR) AF: 0.883 AC: 13469 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3171 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5174 AN: 5178

South Asian (SAS) AF: 0.900 AC: 4343 AN: 4828

European-Finnish (FIN) AF: 0.904 AC: 9574 AN: 10588

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61600 AN: 67998

Other (OTH) AF: 0.830 AC: 1753 AN: 2112

Alfa AF: 0.838 Hom.: 7117

Bravo AF: 0.797

Asia WGS AF: 0.929 AC: 3231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.9
DANN	Benign	0.56
PhyloP100		-0.29
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: rs4350226; hg19: chr1-197132378;