rs2903265

Variant names:

• chr15-80121042-A-G
• rs2903265
• NM_019006.4:c.154+544A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019006.4. 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
	ZFAND6	NM_019006.4	MANE Select	c.154+544A>G		intron	N/A	NP_061879.2
	ZFAND6	NM_001242911.2		c.154+544A>G		intron	N/A	NP_001229840.1	Q6FIF0-1
	ZFAND6	NM_001242912.2		c.154+544A>G		intron	N/A	NP_001229841.1	Q6FIF0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFAND6	ENST00000261749.11	TSL:1 MANE Select	c.154+544A>G		intron	N/A	ENSP00000261749.6	Q6FIF0-1
	ZFAND6	ENST00000558494.5	TSL:1	c.154+544A>G		intron	N/A	ENSP00000454137.1	Q6FIF0-1
	ZFAND6	ENST00000559835.5	TSL:1	c.154+544A>G		intron	N/A	ENSP00000453291.1	Q6FIF0-1

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

African (AFR) AF: 0.591 AC: 24483 AN: 41446

American (AMR) AF: 0.789 AC: 12058 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2409 AN: 3466

East Asian (EAS) AF: 0.499 AC: 2578 AN: 5164

South Asian (SAS) AF: 0.705 AC: 3400 AN: 4824

European-Finnish (FIN) AF: 0.686 AC: 7244 AN: 10566

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49290 AN: 67938

Other (OTH) AF: 0.685 AC: 1446 AN: 2112

Alfa AF: 0.711 Hom.: 32503

Bravo AF: 0.684

Asia WGS AF: 0.644 AC: 2240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.67
PhyloP100		-1.1
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: rs2903265; hg19: chr15-80413384;