rs2903265

Positions:

• chr15-80121042-A-G

Variant summary

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

The NM_019006.4(ZFAND6):​c.154+544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,000 control chromosomes in the GnomAD database, including 35,722 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 0.68 (35722 hom., cov: 32)
• Consequence: ZFAND6 NM_019006.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFAND6	NM_019006.4	c.154+544A>G		intron_variant		ENST00000261749.11	NP_061879.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFAND6	ENST00000261749.11	c.154+544A>G		intron_variant		1	NM_019006.4	ENSP00000261749.6

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103562 AN: 151882 Hom.: 35702 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.682 AC: 103624 AN: 152000 Hom.: 35722 Cov.: 32 AF XY: 0.681 AC XY: 50595 AN XY: 74298

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.685

Alfa AF: 0.715 Hom.: 22745

Bravo AF: 0.684

Asia WGS AF: 0.644 AC: 2240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.67

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: rs2903265; hg19: chr15-80413384;