chr8-134777684-G-T

Variant names:

• chr8-134777684-G-T
• rs4386936
• ENST00000688995.2:n.143-15032C>A

Variant summary

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

The ENST00000688995.2(ENSG00000289405):​n.143-15032C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,100 control chromosomes in the GnomAD database, including 42,959 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 0.75 (42959 hom., cov: 32)
• Consequence: ENSG00000289405 ENST00000688995.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 1 publications found

Genes affected

ENSG00000289405 (HGNC:56081):

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688995.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289405	ENST00000688995.2		n.143-15032C>A		intron	N/A
	ENSG00000289405	ENST00000773977.1		n.116-15032C>A		intron	N/A
	ENSG00000289405	ENST00000773978.1		n.114+786C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113790 AN: 151982 Hom.: 42902 Cov.: 32

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.749 AC: 113907 AN: 152100 Hom.: 42959 Cov.: 32 AF XY: 0.750 AC XY: 55737 AN XY: 74364

African (AFR) AF: 0.836 AC: 34711 AN: 41508

American (AMR) AF: 0.756 AC: 11553 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2630 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3230 AN: 5170

South Asian (SAS) AF: 0.756 AC: 3632 AN: 4804

European-Finnish (FIN) AF: 0.742 AC: 7847 AN: 10576

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.706 AC: 47990 AN: 67978

Other (OTH) AF: 0.747 AC: 1574 AN: 2108

Alfa AF: 0.734 Hom.: 5118

Bravo AF: 0.749

Asia WGS AF: 0.725 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.18
PhyloP100		0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4386936; hg19: chr8-135789927;