8-134554324-C-T

Variant names:

• chr8-134554324-C-T
• rs7827545
• NM_020863.4:c.2976+11009G>A

Variant summary

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

The NM_020863.4(ZFAT):​c.2976+11009G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,836 control chromosomes in the GnomAD database, including 9,610 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 0.35 (9610 hom., cov: 33)
• Consequence: ZFAT NM_020863.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 17 publications found

Genes affected

ZFAT (HGNC:19899): (zinc finger and AT-hook domain containing) This gene encodes a protein that likely binds DNA and functions as a transcriptional regulator involved in apoptosis and cell survival. This gene resides in a susceptibility locus for autoimmune thyroid disease (AITD) on chromosome 8q24. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Nov 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020863.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAT	NM_020863.4	MANE Select	c.2976+11009G>A		intron	N/A	NP_065914.2
	ZFAT	NM_001029939.4		c.2940+11009G>A		intron	N/A	NP_001025110.2	Q9P243-2
	ZFAT	NM_001167583.3		c.2940+11009G>A		intron	N/A	NP_001161055.1	Q9P243-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAT	ENST00000377838.8	TSL:1 MANE Select	c.2976+11009G>A		intron	N/A	ENSP00000367069.3	Q9P243-1
	ZFAT	ENST00000520214.5	TSL:1	c.2940+11009G>A		intron	N/A	ENSP00000428483.1	Q9P243-2
	ZFAT	ENST00000520727.5	TSL:1	c.2940+11009G>A		intron	N/A	ENSP00000427831.1	Q9P243-2

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53248 AN: 151718 Hom.: 9599 Cov.: 33

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.351 AC: 53300 AN: 151836 Hom.: 9610 Cov.: 33 AF XY: 0.354 AC XY: 26293 AN XY: 74194

African (AFR) AF: 0.362 AC: 14985 AN: 41396

American (AMR) AF: 0.355 AC: 5409 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.668 AC: 3428 AN: 5132

South Asian (SAS) AF: 0.460 AC: 2217 AN: 4820

European-Finnish (FIN) AF: 0.367 AC: 3867 AN: 10534

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21519 AN: 67914

Other (OTH) AF: 0.348 AC: 735 AN: 2112

Alfa AF: 0.325 Hom.: 16452

Bravo AF: 0.350

Asia WGS AF: 0.542 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.76
PhyloP100		0.12
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: rs7827545; hg19: chr8-135566567;