rs11634397

Variant names:

• chr15-80139880-A-G
• rs11634397
• ENST00000559157.6:c.*2252A>G

Variant summary

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

The ENST00000559157.6(ZFAND6):​c.*2252A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,082 control chromosomes in the GnomAD database, including 25,454 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 0.56 (25454 hom., cov: 32)
• Consequence: ZFAND6 ENST00000559157.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 163 publications found

Genes affected

ZFAND6 (HGNC:30164): (zinc finger AN1-type containing 6) Predicted to enable polyubiquitin modification-dependent protein binding activity. Involved in cellular response to tumor necrosis factor; negative regulation of apoptotic process; and regulation of I-kappaB kinase/NF-kappaB signaling. Predicted to be located in cytosol. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559157.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAND6	ENST00000559157.6	TSL:2	c.*2252A>G		3_prime_UTR	Exon 7 of 7	ENSP00000454152.1	Q6FIF0-2

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85682 AN: 151964 Hom.: 25453 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.0906

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.564 AC: 85715 AN: 152082 Hom.: 25454 Cov.: 32 AF XY: 0.558 AC XY: 41524 AN XY: 74360

African (AFR) AF: 0.436 AC: 18089 AN: 41466

American (AMR) AF: 0.603 AC: 9215 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2138 AN: 3472

East Asian (EAS) AF: 0.0910 AC: 472 AN: 5188

South Asian (SAS) AF: 0.555 AC: 2675 AN: 4824

European-Finnish (FIN) AF: 0.602 AC: 6358 AN: 10570

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44920 AN: 67956

Other (OTH) AF: 0.570 AC: 1206 AN: 2114

Alfa AF: 0.617 Hom.: 118011

Bravo AF: 0.554

Asia WGS AF: 0.371 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.79
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs11634397; hg19: chr15-80432222;